Universes Collide 3: Shadow Conflicts
by general MB
Summary: With the Master Chief gone, Blue team must forge on alone, and face a new threat. Meanwhile, the Chief and the USS Gettysburg are caught in a war and must ally with their last best hope for victory. -ON HOLD-
1. Chapter 1: business as usual

**If you haven't read the first two universes collide stories, then you better get started**

**Seasons greetings from the general: **here's my Christmas gift to you readers, the thrilling conclusion to the cliffhanger at the end of universes collide 2. Please remember to read and review.

**Disclaimer: I don't own Halo or any other videogame or TV show in this fic**

**chapter 1: business as usual**

**September 28, 2555**

**location: the twelve colonies system, planet Caprica **

Samuel T Anders and what was left of his resistance group flee through the woods, a Cylon hunter-killer party dead on their tracks. Their base at an old high school had been overrun 12 hours earlier and Anders lost most of his people. They were down to about forty armed defectives and quite a few wounded.

"Anders" one of his men said to get his attention, "movement up ahead, doesn't sound like toasters".

"Skin jobs" Anders muttered "spread out".

The Cylons had the ability to create human looking forms of themselves, but not a lot and they didn't vary. The Cylons didn't usually send skin jobs for infantry work, that was handled by their more robotic centurions. But Anders could clearly see some of the approaching hostiles, dressed in full combat gear, colonial marine combat gear... could it be. Sure enough his suspicions were confirmed by the sound of a familiar voice.

"You got a Samuel T Anders over there?" The voice asked, the voice of Helo, a pilot he'd met several months earlier, which could mean only one thing. He stood up and waved his squad over. Leading them was Kara Thrace, who Anders had entered into a relationship with during her brief stint on Caprica several months earlier. She went over tho him and gave him a hug.

"Told you I'd be back" she said "we've got marines and Raptors. Where's the rest of your group?"

"Cylons ambushed us earlier today, what you see is what we got" Anders said.

But their reunion was cut short as another familiar face, the Cylon Sharon who defected from the Cylons and had helped out Anders before screamed "incoming!". Sure enough, the Cylons had triangulated their position and were launching mortars. A few people were injured and Thrace could hear the familiar clanking sound of approaching Cylon centurions.

"They've got us surrounded" Helo said "we're cut off".

Thrace handed Sharon a gun and started falling back to a moldering structure that would offer them some protection. A couple more resistance members were hit as they dove over the wall for cover, med techs began treating them. Kara stuck her rifle through a hole in the wall and started laying down a suppressing fire. Helo was using a small hand held radio to contact someone, Anders had never seen the design before.

"We're pinned down, rescue would be appreciated" he screamed into the small device.

"_We told you not to go alone"_ another voice came through "_stand by, they're on the way"._

_They?_ Anders wondered.

"Give me the rifle" Kara said and in seconds, another marine produced an odd looking rifle from his pack. It was blue and it looked like two fish staked upon one another, with a grip going between them. Karat hit something on the top and a beam of light appeared, connecting the two tips of the rifle. She pointed it through the hole and a whine emitted from the gun as she fired what appeared to be bolts of energy at the Cylons, causing tremendous damage.

"Kara, what the frack is that!?" Anders said in surprise.

"Some new toys we picked up" Thrace replied "along with some friends".

Suddenly a green blur hurled over Anders' head and smacked into a centurion. The figure looked like a centurion itself, it was tall and covered in green armor plates. But unlike a Cylon, it had a great gold visor for an eye instead of the red Cylon one. It hefted some kind of weapon that fired bullets instead of the energy bolts that Kara's used. Another figure landed in the ruin next to Anders, identical to the one that crunched a centurion but this one carried a long barrel weapon with a rectangular scope affixed on the top. Several more figures appeared but these wore black body armor and their faces were obscured by matching helmets, they carried weapons similar to the one the green robots were using. They started firing as did the one next to Anders.

"Linda, where the frack is Kelly?" Kara asked as she continued to fire her rifle.

"She's flanking with blue-four and five" the armored thing next to Anders replied, in a female voice. He looked out again and caught sight of another green blur taking out the mortar positions. Others were also exploding but Anders couldn't identify the source.

"We're clear" Helo said.

"Lets double time to the LZ" said Thrace as she grabbed Anders by the collar and pulled him out of his daze. They ran with the armored giants in the lead and the one who took out the mortars in the back, surrounding them were the black armored figures he overheard Helo call "helljumpers". Eventually the group reached a clearing where several Raptors and other strange craft were parked, guarded by more of these "helljumpers". Kara led Anders over to one, they were larger that the Raptor and had short stubby wings and four engines, two mounted on the wings and two on the tail. Kara had him climb up the ramp into the back and the green giants, Helo and Sharon got in with him. One of the giants and Kara went through a door at the back that presumably contained the cockpit. Before the back ramp closed, Anders saw two ripples in mid air that suddenly appeared as human figures wearing green armor and giant gold faceplates. They sat down in the seats and Anders felt a lurch as the dropship lifted off the dirt with the others like it and the Raptors. Anders stood up and went through the open door into the cockpit and saw one of the green giants was seated in a chair above him on his left and Kara was in the one directly beneath it. Anders found a handhold and grabbed it as the dropship skyrocketed through the atmosphere and into space.

"Where the hell is he?" Kara said under her breath "Kelly, do a scan".

"I'm not... hang on. Three baseships, they've got him" the armored giant behind Kara said.

"Looks like its going to be a rough landing" she said to Anders after realizing he was there "you might want to sit down".

Anders had no intention of missing what came next, as the convoy of Raptors and strange dropships which he learned were called 'pelicans' came around Caprica, he spotted three of the newer Cylon baseships in a heated battle with something that made Anders' jaw drop. A Battlestar, but it wasn't the kind that Kara served on, _Galactica_ was old from what Anders had been told. This Battlestar was one of the newer ones Anders had only caught glimpses at before, _Mercury_ class. Brazened on one of its flightpods was the ship's name, _Pegasus._ They were holding their own against the baseships, missiles and guns blazing. Their Vipers were engaging their Cylon counterparts in a fierce dogfight. Suddenly, one of the baseships exploded, which surprised Kara and Anders, even Kelly.

--

In the CIC of Pegasus, its CO Commander Lee Adama watched the DRADIS screen as one of the Cylon baseships winked away, destroyed, but not by _Pegasus'_ weapons.

"What the frack was that?" His XO, Major Kendra Shaw said from her position across from him

"I don't care if the toasters blew up one of their own ships" Lee said "we need to leave". He picked up the phone and issued the recall order to the fighters while Shaw ordered the FTL drive be spooled up.

--

"_Kara you got two minutes before we jump"_ Lee said over the radio _"get aboard, now"_.

"Wilko, actual" Kara said as she pitched the dropship down through _Pegasus_' flack barrier, the other pelicans and Raptors following her suicidal move. The Cylon raiders began to try and swarm them as they made their approach and the vipers started shooting a hole through them. One raider looked like it was on a ballistic trajectory with their pelican and Anders could see it had the same kind of red eye that the centurions had. The raider stopped short of ramming them and its eye focused on everyone in the cockpit. Anders could feel something tug at his soul as the eye hovered there for a few seconds. The raider veered away as did the rest of them, which gave them a clear path to the flight pod. They weaved through the explosions and made it into the hangar pod with the rest of their group and the Pegasus airwing. The pelican settled into a hover before touching down on the landing deck with the rest of the SAR team.

"Stand by for jump" Kara warned as the familiar bright flash of light and the warping of space appeared outside the pod. The Battlestar jumped and the space outside was tranquil and calm. Kara got out of her seat as did the armored giant called Kelly. Anders had enough of this situation so he pulled a gun on Kelly. He herd several gun bolts being snapped behind him as the rest of the green armored figures snapped their weapons up and pointed them at Anders.

"Kara, what the frack are these things? Where did you get these ships, let alone the Battlestar?" he barked.

"Show him" Kara said to Kelly. She nodded and reached up, twisted her head sideways and pulled off what Anders thought was its head, but turned out to be a helmet. Anders lowered his weapon as a human face stared back at him, she had pail skin and a mane of brown hair. There was also a look of sadness in her eyes, as if she'd lost something dear to her. Anders had seen that look many times among the various resistance members who lost family and spouses to the Cylons.

"Who are they?" he asked "where did you find them?"

"Earth" Kara replied "we found Earth. I've been there".

"Ok, then could you tell me what the frack _that_ is?" he said as he pointed his gun in the general direction of the object floating right in front of the pelican.


	2. Chapter 2: lost in space

**Disclaimer: I don't own Halo or any other videogame or TV show mentioned in this fic. **

**Chapter 2: lost in space**

**July 31, 2555**

**location: somewhere in open space**

In this desolate region of space, nothing moved, there were no star systems, nothing... except one thing. Hanging dead in space was a majestic starship. Its hull bore scars of a recent battle with Forerunner separatists, a few breaches and a gash in its secondary hull where an intense shockwave had hit. On the top of its primary hull was the ship's identifying markings, USS _Gettysburg_ NCC-61591. This cruiser was from a parallel universe that had become trapped where it is now. Their warp engines and long range communications damaged beyond repair. Its crew in stasis to await rescue as its short range COM burped a continuous message, hoping someone would answer. All its running lights were still active but all the lights in the external portholes were dark. Inside the ship, the corridors were on minimal illumination, not a problem for its sole caretaker. A man slowly traversed the halls while working on his padd. He had black hair but was bald on the top, he wore a starfleet uniform with a blue undershirt, indicating he was a doctor. He also had a small triangular device on his right forearm, his mobile holoemitter, for this man was actually a hologram. He was simply called Doctor or Doc as he colleagues on the USS _Voyager_ had called him during its 7 year odyssey through the delta quadrant. During that trek, _Voyager_ had a similar situation where the crew was in stasis to protect them as she ship traversed a deadly nebula. Now, the Doctor was left by Captain Anderson to watch over the crew of the _Gettysburg_ as they slept. He made rounds around the ship, repaired some of the damaged systems, even took a crack at the warp drive which was hopelessly beyond repair. Whenever he wasn't doing this, he practiced opera on the holodeck or worked from his office in sickbay. He'd just completed his daily checkup of the crew as they stayed in their pods when the computer called him to the bridge, saying the proximity sensors had been tripped. The Doctor ran for the nearest turbolift and took it straight up to deck one, the bridge. The only light in the room came from two consoles, the engineering station on the wall and the helm. The Doctor sat at the helm and activated the viewscreen, on it, a large ribbon of energy appeared, cracking through space.

"Computer, run a scan of the anomaly and identify it".

"Anomaly is phenomenon 87634, named the ribbon"

The historical data on the anomaly appeared on the helm station and the Doctor read it, this phenomenon was in this universe as well as the _Gettysburg_'s home universe. This same phenomenon nearly destroyed the _Enterprise B_ and killed Captain James T Kirk.

"Warning" the computer chimed in. "Vessels detected on the trailing edge of the anomaly".

"How many?"

"Two."

The viewscreen couldn't get an accurate picture but it detected two distinct energy signatures matching a pair of objects, one was around the size of a runabout and the other was a small object around twelve feet in length, an escape pod perhaps? The sensors indicated the smaller object was emitting a rather peculiar energy field before it vanished completely. The larger ship drifted out of the ribbon, sensors indicated it was heavily damaged. The Doctor snapped into action and did something he hadn't in a long time.

"Computer... activate the emergency command hologram". This was a sub program the Doctor built into his own matrix while on _Voyager_. It essentially gave him command level training at the flick of the switch and allowed the Doctor to act as a Captain for the ship in case something drastic happened to the crew. Because the Doctor hadn't tinkered with this program in a while, meant his command scheme uniform hadn't been updated with the new uniform style. So when he changed his gray shoulder top was replaced with a red one and his blue undershirt was replaced by the old light blue one, with four gold pips attached.

"Alert, unidentified ship is transmitting a distress call" the computer reported. "Human lifesign detected".

The Doctor looked over the sensor readings, the human biosign was weak and life support aboard the damaged ship was failing. The doctor's command subroutines told him to get the biosign off the ship and to sickbay, so he had the computer activate the impulse engines so they could get close enough to tractor the ship. As the computer handled this, the Doctor went down to sickbay and prepped one of the biobeds along the wall for arrival. When the computer signaled they were in range it automatically transported the human aboard. A scene that echoed when the _Gettysburg_ found the Master Chief a year ago played out as a large armored figure appeared on the biobed. The human wore large armor with a red and orange color scheme. The shoulders sections were big and bulgy and the faceplate of the helmet was green and in the shape of a chevron. The arms hanged over the side as the width of the biobed was too small for the entire width of the armor. The Doctor scanned the human clad in the armor but the readings were inconclusive as the armor blocked most of his scans. But there was one thing it couldn't block. The Doctor went over to a nearby station and locked onto the lifeform inside the armor and was able to beam it to the main biobed in sickbay. A slender figure appeared lying on the main biobed. The human occupying the armor was female and dressed in a blue, skin tight undersuit. She had a mane of long blond hair. The doctor's scan indicated she was 27 years of age, and something was up with her DNA. The Doctor extracted a sample and had the computer analyze it, he was intrigued by the results, but they also confused him. This situation was to big for he ECH subroutines to handle, he needed to wake the senior staff, if her ship was flyable then they could contact the UNSC and the _Defiant_. He injected their guest with a sedative to make sure she'd stay unconscious before heading down to the pod bay.

--

He stood clad in his combat skin, his hand poised above the large yellow holographic button. He'd entered his override code and the array was armed and ready to fire by remote, from his location at his people's last stand. A monitor hovered next to him, it spoke in a voice that sounded weathered with age and wisdom.

"We have no choice, they must be stopped".

"I know" he replied as he pressed the button. "Forgive me, my love" he muttered.

As quickly as he entered that strange dream, Master Chief Petty Officer John-117 was dragged away as he woke up. The lid of the starfleet stasis pod slid down and the Chief was able to climb out. The other pods in his section, containing the command staff of the USS _Gettysburg_ also opened. He turned to the pod behind him in time to see it open, and a woman dressed in an identical undersuit to John's, sat up. She was Petty Officer Cortana Halsey, a fellow Spartan and John's lover. He was surprised at how the Doctor said going into these pods was like taking a nap, speaking of him, John saw the Doctor. He was operating the main console, but was dressed in a different uniform, one with red shoulders and it lacked the pin striped embroidering, he also sported four rank pips.

"You get promoted?" he asked.

"Not exactly" he replied as he walked over to Captain Anderson who was getting out of his pod.

"Doctor, how long have we been under?" said Anderson as he shook off the last bit of grogginess.

"You've been in stasis only 19 days" the Doctor replied

"I think we're still in stasis" said Commander Lisa Baker as she regained consciousness with Commander Collins and Lieutenant Cheney.

"She's right, doctor as Captain" Cheney chuckled.

"I woke you because 30 minutes ago this appeared in front of the ship". He handed Anderson a padd containing a freeze frame of the ribbon.

Anderson handed the padd back to the Doctor and stood up. The Chief noticed a weird look on his face as he spoke to the Doctor in a low whisper. But John didn't listen in as he turned his attention over to Cortana who was getting out. She wiped a strain of her blue hair out of her face before turning to the Chief.

"How long were we..."

"19 days" John said. "Something happened, my guess isn't rescue".

They didn't even have time to get their armor out of the locker they'd stowed it in as Captain Anderson had every awake officer in the room head for sickbay. Lieutenant Cheney disappeared for a minute as they walked through the corridors and didn't meet up with them when they arrived at sickbay. Commander Collins left them there and headed for engineering as did Commander Baker while everyone else went in. The Doctor showed them the woman he'd found in the ship and her armor. Cheney finally arrived, sipping a cup of coffee he'd slipped away for.

"So what's the big emergen..." he said before noticing the guest on the biobed and the armor on another. He set the coffee down and retrieved a phaser from under one of the tables.

"Relax, Lieutenant" said Anderson. "I don't think she can hurt us".

"Captain, you need to see her DNA" said the Doctor as he brought up her profile on the main display mounted on the wall. "There are sever strands that are non-human, like this". He highlighted one and enhanced it. "From what the computer can tell, these strands are remotely avian".

"Avian?" John asked. "As in a bird?"

"She's part bird?" Anderson said.

"Only a small part, and it only gives her a strong ability to withstand freezing temperatures" the Doctor explained. "There's another that I can't even decode and doesn't match anything in the federation database. This also seems to negate her ability to survive in freezing temperatures. And is coated in a unique energy signature I can't identify either"

"Some kind of botched augmentation?" Cortana said.

"That's what it looks like" said The Doctor. "I can defiantly confirm she wasn't born with it".

"I say its time for some answers" said Anderson. "Wake her".

The Doctor complied and pressed a hypo to her neck. She stirred and immediately reacted to the doctor's presence.

"Relax, I'm a Doctor. You're safe". He moved aside and allowed Anderson to step forward.

"I'm Captain Marc Anderson, you're on board the federation starship _Gettysburg_. We responded to your distress call and brought you aboard".

The woman bounded up and sat on the bed, breathing a sigh of relief.

"Thank god, a federation ship" she said.

"You've herd of us?" Anderson asked.

"Is that some kind of joke?" The woman asked. "By the way, what's with the new uniforms, and the medical facilities?"

"I think you may have us confused with someone else" Anderson said "we're not from your universe".

"What are you talking about?" The woman asked sharply. "You are galactic federation, right?"

"No, united federation of planets" Anderson corrected. "Like I said, we're not from this universe".

"Neither is she" the Doctor said as she finished scanning the strange woman. "Her quantum signature doesn't match the Master Chief or Cortana's".

"What's your name?" Anderson asked.

"Samus" the woman said, still trying to assimilate what she just herd. "Samus Aran".

"Were you attacked?" Anderson asked. "Our Doctor found your ship heavily damaged".

"No" Samus replied. "I hit some kind of an anomaly trying to chase my target".

"What exactly do you do?" John asked as he walked forward. Intrigued at the idea she was a soldier.

Samus had to get over the shock of seeing this half dressed, handsome, muscular man in front of her before she answered John's question. "I'm a bounty hunter" she said. "One of the best in the federation. My federation I guess".

"Who was your target?" John asked.

"Weird guy" Samus said, curious as to why this guy would be asking about someone he's probably never herd of, so it couldn't hurt to tell him. "He doesn't have a name, he's simply called The Doctor."


	3. Chapter 3: puddle jumping

**Message from the general: **from now on, the holographic Doctor is going to be called the EMH. To alleviate confusion.

And what happened to all my loyal reviewers from the first chapter?

**Disclaimer: I don't own Halo or any other videogame or TV show in this fic**

**chapter 3: puddle jumping**

**August 3, 2008**

**location: Pegasus galaxy, Atlantis base **

Richard Woolsey watched from the control room of Atlantis as the Stargate activated, and a puddle jumper descended from the bay above them. In it was Lieutenant Colonel John Sheppard and his team, Doctor Rodney McKay, Teyla and Ronon Dex. McKay had found some lab linked to a project run by the ancients in the Atlantis database. The file was mostly encrypted and only gave the gate address and the fact it was linked to this mysterious project. So he managed to convince Woolsey to approve a mission.

"Colonel, you have a go" said Woolsey.

"See you in twelve hours" said Sheppard as he hit the engines and the jumper glided through the gate. When they emerged, the jumper's drive pods extended and the jumper took too the air, over what remained of a city.

"Rodney?" Sheppard asked.

The HUD appeared on the windscreen and Rodney had a look at the readings.

"There was some kind of explosion here, nuclear judging from all the radiation" McKay reported. "I'd say it probably happened in the past 7 months."

"Perhaps the wraith destroyed the city when they detected it was of ancient origin" said Teyla.

"With a nuke?" Sheppard said. "Not their style, plus the only people they could have stolen one from is the Genii. And we just had contact from them yesterday."

"Travelers?" Ronon suggested.

"Why would Larin blow up an ancient city?" Sheppard said.

"I don't think this is an ancient city" said Rodney as the jumper weaved through the buildings. "The architecture doesn't match."

"I'm going to circle back to the gate" said Sheppard as he prepared to bring the jumper around.

"Whoa, wait a second" said McKay as he noticed something on his tablet PC. "There are ships a few clicks out of the city, moving fast."

"Let's follow then" said Sheppard as he put the jumper into stealth mode and banked up on a parallel course to the bogeys. They reached space where a heated battle was taking place, between familiar friends and foes.

"Pegasus!" Teyla said as they caught sight of the mighty Battlestar. Fighting three Cylon baseships.

"I'm picking up a small group of craft moving toward them" said Rodney. "Some of them are pelicans."

"Rodney, don't tell me we're in a parallel universe, again!" Sheppard said, recalling the previous time they met the colonials and the UNSC. Not to mention a crazy ride on a parallel _Daedalus_ before that.

"The gate's been known to cause jumps to parallel universes before" Rodney said.

"Well how do we fix it!?" Sheppard asked in an annoyed tone.

"I don't know" Rodney said. "We'll have to turn around and go back to the gate so I can access the DHD.

"Perhaps we should consider helping the _Pegasus_first" said Teyla.

"She's right" Ronon muttered.

"All right" Sheppard said. "We'll help them out then see if they can help us out, fair enough?"

Sheppard brought the jumper in toward the nearest baseship and flew along its hull. He deactivated the stealth mode long enough to fire a pair of drones into the ship before re-cloaking and veering away. The drones destroyed the baseship and for some reason, the Cylon fighters began to retreat.

"Where to now?" Ronon asked.

"_Pegasus"_said Sheppard. "If we try and set down near the gate then we can defiantly expect the Cylons to find us. We'll go with them until things settle down and we can come back."

Sheppard weaved through the flack and brought the jumper into one of Pegasus' flight decks. Suddenly a wave of nausea passed over everyone in the jumper and a bright flash filled the interior, then disappeared as quickly as it came.

"What the hell was that?" Sheppard said as he rubbed his eyes.

"FTL jump" Rodney said, remembering the folding space drives the battlestars used. "We're not in orbit of that planet anymore."

"Lets drop in, shall we" said Sheppard as he floated the jumper down to face the cockpit of one of the pelicans. He could see three people inside, having a discussion. He deactivated the stealth generator and the heads of the three in the cockpit turned to look at the jumper, hanging right in front of them.

"Sorry for dropping in like this, folks" Sheppard said over the radio. "We got a little lost and decided to hitch a ride with you."

**

* * *

**

July 31, 2555

**location: USS _Gettysburg_- sickbay**

Most of the people in sickbay reacted in shock to Samus telling who her target was. Enough for the EMH to run another quantum resonance scan.

"Her signature matches the one I took of The Doctor and her companion while they were aboard. She's from his universe". Said the EMH.

"You've met him?" Samus asked.

"Once before" said the Chief. "He helped us out which is why I'm wondering why someone would put a bounty on him."

"I didn't know what my client wanted with him, he or she was anonymous" said Samus. "Just provided a time, place and description of him."

**

* * *

**

Galactic year 2027

**location: planet K117Y**

The tenth Doctor was walking through a bazaar on planet K117Y. A strange name for a planet, but the galactic federation that ruled the galaxy at this point in time preferred a more uniform filing system. The Doctor had just had a mysterious encounter with a time portal inside his TARDIS that led to the Proms in London. After dispatching a Graske that tried to cause a little mayhem, he closed the portal, and suddenly got a message on his psychic paper to travel immediately to planet K117Y in galactic year 2027. So here he was, looking for whoever sent the message. The marketplace was a fairly large street with vendors selling a wide array of local and alien goods. He moved among them, smiling as he went. New alien cultures fascinated him, not as much as humans though. As he passed an alleyway something appeared in his peripheral vision, and he had only seconds to dodge a large orange ball that screamed out of the alleyway. Reaching inside his trenchcoat, The Doctor removed his trusty sonic screwdriver and prepared to defend himself. The ball hit the ground and caused most of the shoppers in the marketplace to flee. The ball came around, like it was somehow tracking The Doctor. He raised his sonic screwdriver, pointed it at the ball and activated it, causing the ball to stop in its tracks. Also the ball seemed to come apart and transform into a large armored figure. The Doctor recognized the design, it was Chozo. An extinct race The Doctor had met some time ago.

"Doctor?" the figure asked. "You're coming with me."

"Sorry, no can do" The Doctor replied in his usual cheerful tone. "I actually have to meet someone, unless you're the one who sent the message to my psychic paper. Which I have to say is rather brilliant."

"Enough" Samus barked. Her right arm transformed into a small cannon, which was pointed at The Doctor. She fired a freeze blast that The Doctor was able to dodge in time. It froze part of the wall he was standing in front of. He used his sonic screwdriver again and disabled the function of her weapon, temporarily, though. Hoping it would be enough to distract her as she reset her suit's systems. The Doctor bolted in the direction of the TARDIS. It wasn't long before Samus caught up with The Doctor outside the TARDIS. He avoided another shot from her freeze beam before making it safely inside the TARDIS doors. Throwing his coat on the hanger, he went up to the center console and engaged the launch sequence. He tried to use the time vortex but was rewarded by an alert, level 2 that indicated a small foreign object was attached to the outside of the TARDIS, a tracking device. The Doctor could only travel in normal space so he left orbit and headed out into the planetary system. But Samus was hot on his tail in her gunship. The Doctor's TARDIS was surprisingly more maneuverable than the gunship, but no match for what happened next. The TARDIS and the gunship were caught in the trailing edge of an anomaly that just appeared out of nowhere. Alarms inside the control room of the TARDIS blared, the lights flickered and The Doctor was thrown backwards into the pilot seat by the impact.

"Oy, then!" The Doctor said to the TARDIS as he reached the controls and began to stabilize the ship. The tracker had been sheared off and The Doctor was able to activate the time stream, disappearing from the edge of the anomaly. The Doctor began to analyze the data and the stabilization process. But as he moved along the console of the TARDIS he noticed someone else hunched over the controls. He was fumbling around when he looked up. The other man was dressed in a cream colored frock coat, striped pants and a cricket uniform that had a set of question marks embroidered on the collar. Also on his coat, worn like a lapel pin... was a stalk of celery.

"What!?" Said The Doctor.

"What!?" Said the stranger.

They walked closer together and looked each other over, not wanting to believe it, but there was no denying it. Standing in front of the tenth doctor... was the fifth doctor, again.

"Oh not this rubbish again" said the fifth, recalling the previous time he ran into his tenth incarnation.

"This can't be right!?" Said the tenth, his face changing to dread.

"What are you talking about?" The fifth asked.

"This, I don't remember it happening" said the tenth.

"Bloody hell" the fifth muttered

Suddenly, the TARDIS was struck yet again and both doctors manned the controls, in a desperate attempt to steer the unwieldy craft.

**

* * *

**

July 31, 2555

**location: USS _Gettysburg_- sickbay**

"So I planted a tracker on the thing and sure enough it took off. I signaled my gunship and then chased after it. Then I got hit by some anomaly, lost consciousness and woke up here."

Samus had just finished retelling her story to the Chief and the other three people in the room. John didn't know what to believe, true he didn't know The Doctor for long but he saved their skins on Earth and in the Dyson sphere. But part of him also felt sorry for Samus, being taken from her home universe and was probably stuck here.

"Well, Ms Aran, I'm sorry to say we don't have any way to send you back" said Anderson. "We'll get you a room if you want until my engineer can take a look at your ship."

"I applicate your hospitality, Captain" said Samus. "But I'm better off helping this engineer of yours."

"Very well then" said Anderson. "Master Chief, I believe you remember the way to the shuttlebay."

"Yes, sir" said the Chief as she hopped off the bed and followed him out. Cortana, Anderson and the EMH were left in sickbay to ponder their latest house guest.

--

The Master Chief, still in his undersuit walked with Samus through the corridors of the _Gettysburg_. He was still uncomfortable, only wearing his undersuit, but Samus was in a similar situation in only her power suit.

"So what do you do on this ship?" She asked as they entered the turbolift and took it to deck ten.

"I'm not a member of the crew" said the Chief. "Me and Cortana are passengers, like you."

"Cortana, she's the blue haired woman you were with?"

"Yes, we're with a different organization called the UNSC" John said who then went on to outline what he was, their recent battle with The Order and how they ended up stranded.

"Nice to find someone I can relate to" said Samus as the turbolift stopped and the pair merged on deck ten, walked a short distance to the shuttlebay and entered. Most of the _Gettysburg's_shuttles were damaged during the battle with The Order. Taking up most of the bay was Samus' battered gunship. John and Samus entered to a stream of charred bulkheads, loose wires and a frustrated Commander Collins as he hunched over an access panel in the floor. A slender, grease covered arm appeared from inside the access panel and Collins handed it a tool.

"What are you doing?" Samus snapped.

"Sorry" said Collins. "We needed to determine if your ship was space worthy. So we could use it to signal for help.

"Which it isn't" said Commander Baker as she emerged from the access panel. "The hyperspace and sublight engines are completely fried."

"And it looks like whatever AI construct this ship had was flatlined by the surge" said Collins as he examined a computer terminal with his tricorder. Samus braced herself against the bulkhead, the Chief noticed this.

"I take it your ship's AI was a friend?" He asked.

"You could say that" she replied. "His name was Adam, after another dead friend. I've got no one now."

The Chief was about to say something when the ship was rocked by something. The resulting tremors caused Samus and the Chief to fall backwards out of the open hatch of her gunship.

--

Captain Anderson, Cortana and the EMH made their way to the bridge. The ship automatically went to red alert after the first impact. When they arrived, the stations on the bridge were dark except for the two the EMH had active. Captain Anderson took the helm while the EMH settled into ops. Cortana sat down in Commander Baker's chair.

"The ribbon" said the hologram. "It somehow caught the ship in its trailing edge."

"Reversing engines" said Anderson as he engaged the impulse engines and tried to break free.

"No effect" said the EMH.

"What's happening?" Cortana asked.

"I don't know" said Anderson. "I've got it! I remember what they did last time. Doctor, arm photon torpedoes and target the closest antimatter discharge."

"Ready" the EMH replied.

"Fire!"

The _Gettysburg_fired three torpedoes in rapid succession at the discharge. But the blast wave enveloped the ship and propelled it outward, the ship tumbled through space until the ribbon was gone from sight. On the bridge, Anderson regained his posture after falling from his seat. Cortana as well.

"Report" Anderson asked the EMH, who somehow remained in his chair.

"We've stopped. All systems seem to be online and the shields protected us from the worst of the ribbon."

"What exactly is the ribbon?" Cortana asked.

"Its a spacial anomaly in my universe" said Anderson. "and apparently its in yours, too."

"Captain, I think we have taken some damage" said the EMH. "The navigation sensors are malfunctioning. According to the starfix, we're in the Epsilon Eridani system."

"Reach!?" Said Cortana. "We're back in UNSC space!"

"The ribbon only moves at warp 2" said Anderson. "I don't see how it could have transported us, not to mention follow us and hit us the first time."

"Captain, we've got ships approaching" said the EMH. "One dozen vessels in total. They're ten meters in length and don't have any kind of shielding."

Anderson settled back into the helm and activated the viewscreen. 12, X shaped fighters made their way toward the _Gettysburg._

"They're hailing us."

"On speakers" said Anderson.

"_Attention, unknown vessel, this is delta squadron. You've penetrated our airspace and are required to follow us back to our base. Acknowledge this signal." _

"I guess we open a channel" said Anderson. The EMH complied and the Captain spoke. "This is the federation starship _Gettysburg_, we here you and will comply with your request."

"Captain, is this a good idea?" Cortana asked. "We don't know who these people are."

"You said this was a UNSC system?" Anderson asked.

"Well yes" said Cortana. "But its been abandoned. Reach was glassed during the war."

"There must still be a UNSC presence?"

"I'm not sure" said Cortana. "Perhaps a monitoring buoy over the planet."

"That's good enough for me" said Anderson. "According to these sensors, those fighters are nowhere near as fast as us. And their weapons wouldn't do much against our shields. Looks like we're leaving them in our dust."

He went to lay in a course away from the mysterious fighters, but the EMH pointed out they were picking up another communication, broadcasting on all frequencies. Anderson piped it in.

"_... I say again, raider forces have attacked in full. We're taking damaged to several sectors of the hull. Repeat, to any ships in grid Epsilon, this is Babylon 5. We're under attack!"_


	4. Chapter 4: signs and portents

**Disclaimer: I don't Halo or any other videogame or TV show in this fic**

**chapter 4: signs and portents**

**January 14, 2261**

**location: Epsilon Eridani system, Epsilon III- Babylon 5**

Commander Susan Ivanova's week had been nothing but pleasant. Morale had been at an all time low since the tragic death of their station's commanding officer, Captain John Sheridan a couple of weeks earlier. Today, the raiders launched an unprecedented attack against the station after and independent freighter had to be escorted to the station by starfuries, only to be ambushed by a raider carrier that suddenly opened a jump point off of the station. Babylon 5 had fought a similar ship 3 years earlier, but this one had weapons this time around, not to mention twice the complement of fighters. Unfortunately for the station, no warships were present, but there were a few white stars on patrol in the local grid. One of the first things Ivanova did upon reaching Babylon 5's command and control center or C&C was to transmit a distress call to any warship of one of the league of non aligned worlds, that usually lurked nearby.

"Lieutenant?" Ivanova said to Lieutenant David Corwin, the station's operation's Officer. "Any activity at the jumpgate?"

"Negative, ma'am" he replied. Suddenly the whole room shook as weapons fire struck the hull.

"Interceptors are running hot" Corwin reported. "Their weapons fire is getting through."

Ivanova furiously typed in commands into the console before her, retransmitting the distress call she just recorded. She cursed under her breath, Ivanova had ordered one of their best starfury squadrons to investigate some unusual energy readings halfway to sector 14. B5 was left with only two squadrons to defend against the raider fighters, which left the station's defense grid to handle the carrier, but it was using some kind of jamming technology to prevent a targeting lock.

"Commander, perhaps we should consider giving them the shipment of quantium-40" said Corwin.

"I'm not giving into some bold raider's plan, plus we need that shipment. If we let them get away, it would show any thug that Babylon 5 is a pushover. What would the Captain do if he was still here? ETA on delta squadron?"

"I can't raise them" Corwin said. "The raiders just blanketed all channels with static. And I'm also picking up a large contact approaching."

"Great, now they're using sensor ghosts" Ivanova remarked.

"This isn't a sensor ghost" Corwin said. "The contact is approaching fast, configuration is unknown."

"Lets see it" Ivanova said. Corwin piped the feed from the external cameras into Ivanova's monitor, due to the blast door over the main window in C&C. "What the hell?" Ivanova muttered.

--

The _Gettysburg_ approached the area where the distress call was sent and slowed down when they detected contacts.

"Report?" Anderson asked, still seated at the helm.

"According to Cortana, this is where that Reach planet should be. But this planet is class L" said the EMH.

"That has to be it" Cortana said. "Reach isn't habitable anymore."

"Cortana, the sensors are telling me that this planet has been uninhabited for some time" said Anderson. "It wasn't made this way by artificial means."

"So then where are we?" Cortana asked.

"Captain, those contacts are entering visual range" said the EMH.

"Put them up" Anderson ordered.

The viewscreen activated and zoomed in on a heated battle in progress between more of the X shaped fighters and several delta shaped fighters. Also present was a larger ship that appeared to house the delta fighters. It was attacking something much larger. At first glance, it appeared to be a ship, but the lack of engines indicated it was a space station. It was roughly cylindrical, had a spherical section attached at the front and a spinal column running along its top. Toward the back were two sets of six panels each, which protruded like fins. At the back appeared to be a long tail sticking out that gave off a radioactive signature, a power source for the station.

"Ok, who sent the distress call and who's the aggressor?" said Anderson.

"I think its obvious" Cortana said. "That space station is being attacked."

"Yes but the prime directive applies in this case. We know nothing about these people or their conflict."

"Captain, that station has over 250,000 lifesigns aboard" said the EMH.

"Run a quantum resonance scan" Anderson ordered.

The EMH typed away at the controls and in less than a minute the computer had the results. The hologram looked over at the Captain and simply nodded. Anderson let out a long sigh, they were once again in a different universe, now even further cut off from Starfleet.

"What are you going to do this time, Captain?" Cortana asked in an annoyed tone. "You going to wait until one of those ships decides to take a shot at us before you violate your precious prime directive? Or are you going to do what we both know is the right thing."

Anderson stared long and hard at Cortana before turning back to the controls, taking a deep breath and exhaling it. "This is probably a court-marshalable offense, but who's going to stop us. Doctor, arm phasers, I'm taking us in."

--

"Commander, the ship is accelerating again!" Said Corwin.

"Stand by to re-target the defense grid on it if it fires on our fighters" Ivanova ordered.

"Three raider fighters are breaking off and turning to engage the unknown."

Ivanova watched on her monitor as the fighters accelerated head on to face the new ship. They fired their weapons at the ship, but Ivanova was surprised at what happened next. The weapons fire struck some kind of barrier in front of the new ship and the fighters veered away from it. The new ship kept on coming and suddenly a crimson orange beam emitted from the oval shaped front, and struck the raider carrier, slicing clean through it. The raider ship tumbled through space, all power systems dead.

"What the hell was that?!" Ivanova said.

"Unknown" Corwin reported. "Some kind of high energy output associated with that beam."

"ETA on those white stars?" Ivanova asked. "I don't want to get caught with our pants down if this new ship decides to take a shot at the station."

"Should be any minute" Corwin said. "Commander, the remaining raiders are signaling us, they want to discuss the terms of their surrender!"

"What about the other ship?"

"Its holding position 300 kilometers off the station. Scanners can't penetrate the barrier around it, so I couldn't tell if they're going to power up their weapons."

"We're going to have to keep them distracted until those white stars show up, then we'll have some options available" said Ivanova. "Open a channel to them."

--

"I'm intercepting communication from those delta shaped fighters offering a full surrender to the space station" said the EMH.

"Now we see what they want from us" said Anderson. "Open a channel."

"Captain, they're hailing us" said the EMH.

"Put them on, audio only."

"_Attention unknown vessel, this Commander Susan Ivanova of Babylon 5. Please identify yourself."_

"This is Captain Marc Anderson of the federation starship Gettysburg, we're here in response to your distress call. I would be happy to explain more, perhaps in person."

"_uh... very well, come aboard in one hour. Babylon control, out."_

"Get Cheney up here" Anderson said to the EMH. "And, Cortana, you might want to change into something a little less revealing."

Cortana blushed slightly as she got out of Commander Baker's chair and made her way to the turbo shaft. Anderson rose from the helm and sat down in his chair, then keyed the COM.

"Anderson to Collins."

--

In the shuttle bay, Samus was regaining consciousness after bumping her head on the fall from her gunship. Sue suddenly realized she'd landed on top of John who was also beginning to stir. Samus quickly got off him and offered a hand to help him up.

"Do you know what happened?" He asked.

"No, felt like the ship was hit by something" Samus replied.

They both turned their heads in the direction of the gunship as someone screamed "ouch!" A moment later, commanders Baker and Collins emerged, Collins was massaging his right shoulder.

"He was knocked around inside, dislocated his shoulder" Baker explained. "I just put it back."

"You could have counted to three, first" Collins retorted.

"_Anderson to Collins"_

Collins slapped his communicator and replied "here, Captain."

"_Find Baker and the Master Chief, we're having a staff meeting in ten minutes." _

--

After settling Samus with some quarters, John, Collins and Baker came up to the observation lounge where Cortana dressed in a jumpsuit and Anderson were the only other ones present.

"The Doctor is supervising the revival of the rest of the crew, and Cheney is running an analysis of Ms Aran's armor" Anderson said as everyone took a seat. Anderson brought everyone else up to speed on what had happened with the ribbon and Babylon 5.

"so what exactly is the ribbon?" John asked.

The Captain stood up and walked over to the display mounted on the wall, then activated it. Several images of the ribbon appeared.

"Its a spacial anomaly in my universe and apparently it was in yours and Samus'. We didn't know it was capable of transporting people to parallel universes."

"Well then what did it do?" Cortana asked.

According to the report, the ribbon is supposed to be a doorway to something called the nexus. Its an entirely different dimension of existence where if one were to enter, their wildest fantasies, all their desires... could become reality" Anderson explained. "In my universe, eight years ago a man called Soran attempted to get into the nexus by altering its trajectory to intersect an M-class planet. He was thwarted by the starship _Enterprise._ Anderson paused for a moment and took in a deep breath before continuing. So the question isn't how we got here its what we do now?

"Captain, if I may" said Cortana. "I know I'm not a member of your crew..."

"you and the Chief are as much a part of this crew as I am, Cortana" Anderson said. "Go ahead and continue."

"Sir, what about this Babylon 5 station. They seem as good as allies we're going to get in this universe."

"My thought exactly, I'm going over to their station in twenty minutes to begin talks with their Commander. Hopefully, we may be able to secure some kind of alliance, this ship still isn't in top shape after the battle with The Order, their facilities could help Collins expedite repairs."

"Captain I know security is Cheney's department" said Baker. "But my recommendation is to take at least one of the Spartans with you, just in case."

"Captain, I volunteer" said John as he stood up, still in his undersuit.

"I appreciate it, Master Chief" said Anderson "and I was going to suggest you come along, but I recommend you not wear the armor, we don't want to scare these people. I have something in mind for you... but first". He hit his communicator. "Anderson to doctor."

"_Go ahead, Captain."_

"how many of the crew have you revived?"

"_Ninety-three"_

"Is Ensign Nicole Baker awake?" Anderson asked.

"_She was one of the first people I revived"_ the EMH replied.

"Have her and any transporter technicians that are up report to transporter room three in fifteen minutes."

"_Aye, Captain."_

"Baker?" Cortana asked the Commander who shrugged when the Captain said her name.

"She's my younger half-sister" Baker replied.

"I recommend you keep family business separate from this for now" said Anderson. "Dismissed."

Everyone left their seats and went out the doors to the bridge, except John who approached the Captain.

"Sir, do you know more about this ribbon then you're letting on? When you got to the part about that other ship, the _Enterprise..."_

"My older brother was on the _Enterprise_. When they tried to stop Soran some of his allies attempted to disable the _Enterprise_. They succeeded in starting a core breach... my brother didn't get out in time."

"I'm sorry" John said.

"Don't, it was a long time ago" said Anderson.

Captain! John said as he pointed out the observation lounge windows. Three blue funnels appeared in space, and a strange craft exited each. They were slightly pinkish in color but also had shades of blue. The whole craft vaguely reminded John of a bird.

"I think I'll speak to Commander Ivanova about that when we meet her" said Anderson. "Anyway, we need to get you fitted."

--

A few minutes later, John and Cortana were in the transporter room, Cortana was clad in her armor finally. But John wore a freshly replicated Starfleet uniform to 'blend in' with the away team.

"The collar itches" he mumbled.

"You look great" Cortana replied.

"You remember how to use one of these, right?" Cheney asked as he handed John a hand phaser.

"Yes" John replied as he slid the phaser into the holster on his waist. The transporter room doors opened and Captain Anderson walked in with a shorter girl probably no older than 21, and she bore a striking resemblance to Commander Baker.

"Look, Captain, I don't think I'm the right person for this. I work in stellar cartography" she said.

"Captain, why is she here?" the Chief asked.

"Ensign Baker is half-Betazoid" said Anderson.

"What's a Betazoid?" Cortana asked.

"Betazoids are empathic as opposed to telepathic, we have the ability to read people's emotions but cannot enter someone's mind like a Vulcan can" Nicole said.

Cortana looked closer with her enhanced vision and was able to see her iris was completely black.

"Shale we?" Anderson said as he directed Nicole and the Chief to step onto the transporter platform while he stood next to the transporter technician.

"I just have to make a call first."

**

* * *

**

January 14, 2261

**location: Epsilon Eridani system, Epsilon III, Babylon 5- Captain Sheridan's office **

Commander Ivanova wasn't comfortable using Sheridan's office, but SOP dictated that all first contact meeting were to be done in the captain's office, since it was the largest. Gathered in the office was acting security Chief Zach Allan, filling in while Garibaldi was MIA. Also there was Minbari ambassador Delenn, she had taken Sheridan's death the hardest. Just walking in was Lyta Alexander, the station's resident telepath and assistant to the Vorlon ambassador.

"Delenn, you're sure the Minbari have never encountered a ship like this?" Ivanova asked.

"My people have seen their fair share of strange vessels, but none such as this" Delenn replied. "You said the markings were in human English?"

"Yes, the ship is even called the Gettysburg, after the civil war battle. But this has to be a telepathic" ruse said Ivanova.

"I'm not detecting a telepathic field" said Lyta. "In order to produce an illusion of that size would take a strong enough field that even a P-2 could detect."

"Zach, what about the security arrangements?"

"I've got a path cleared from the hangar bay right to here for when their shuttle docks."

"Good, they should be coming over soon, we may have to arrange quarters in the alien sector if they decide to stay on the station. Doctor Franklin will also need their atmosphere requirements."

"_C&C to Ivanova"_

Ivanova activated the link on her hand, "Ivanova, go."

"_The Captain of the alien ship wants to talk to you."_

"Put him on then"

"_Commander Ivanova? You'll forgive us, we're going to be there in a minute, we just need to trace your COM signal."_

"Wait, my COM signal?"

"Commander!" Zach barked as he drew his PPG. Ivanova watched as three columns of blue swirling energy appeared in the office that resolved into three figures. Ivanova couldn't believe it, they were human! Two males and a female, they wore strange black uniforms that had gray along the shoulder area and across the chest. On their chests were strange looking pins and on their belts were boxed shaped devices. Although the tall one had what looked like a weapon on his.

"Sorry for the sudden intrusion, transporters are a much easier way to travel, I'm Captain Anderson."

"Sorry, Captain, we just didn't think you were human" said Ivanova.

"Let me first say that we're from what is called a parallel universe" Anderson started.

"I'm familiar with the concept" Ivanova replied.

"Well how we got here is somewhat of an accident, and right now we're looking for allies who know this part of space. To put it simple, we're looking for an alliance between my ship and your station."

"Go on" Ivanova said.

"Wait, Captain!" Nicole said. "That one", she pointed to Lyta. "she's telepathic."

"How the hell did you know that?" Ivanova asked.

"So is she" Nicole said as she pointed to Ivanova. "Just nowhere near as strong."

"That's fine, Ensign, any deception?" Anderson asked.

"No, sir, they're sincere about an alliance if we offer it."

"I see humans in your universe are also telepathic" said Ivanova.

"No" Nicole replied. "I'm only half-human, my mother was a member of a telepathic species."

"Perhaps we should get on with the terms of this alliance" said Anderson. "I am willing to offer my ship to help protect this station from any threat you may face, we cannot however share our technology or assist you in military conflicts. We can offer humanitarian aid in the form of food and medical care.

"And in exchange?" Ivanova asked.

"I want to use your station as a base for my ship during our stay, she was heavily damaged in a recent conflict and we need a port facility to help expedite repairs. My engineer also asked if you had any materials like these."

Anderson handed a padd with a list of several compounds and their chemical compositions to Ivanova.

"I can take a look, why?"

"Our warp drive has been damaged and we need these compounds to fashion replace parts for it" Anderson explained.

"What's a 'warp drive'?" Zach asked.

"Our faster than light propulsion" said Anderson.

"You don't use hyperspace?" Ivanova asked.

"I have herd of it, but warp drive is a much more efficient means of travel for us".

"Commander if I may" said Delenn as she lowered her voice to a bare whisper. "We should be asking these people for help in our battle with the shadows. Their weapons are more advanced than we've ever seen and they could help turn the tide of this war."

"Excuse me" said Anderson. "I have excellent hearing. Now... what are 'the shadows'?"


	5. Chapter 5: there and back again

**Message from the general: Apologies** for this being so late, I was swamped with mid-terms and a play. Also, I have seen the premiere episode of Battlestar Galactica, and it was epic. So to answer your question, I have no intention of using any of that material in this fic as I have already established a connection for BSG to Halo... but I'm not so sure about Ellen Tigh.

**Disclaimer: I don't own Halo or any other videogame or TV show in this fic**

**chapter 5: there and back again**

**date unknown**

**location: TARDIS **

Both the tenth doctor and the fifth doctor tried desperately to regain control of the TARDIS, neither caring how the fifth somehow arrived. The TARDIS finally came to a stop and the tenth doctor moved over to the display screen to analyze the reading of whatever anomaly they hit.

"Doctor, our TARDISes must have merged again" said the fifth as he stood next to the tenth. "We need to separate them!"

"Hold your horses, doctor" said the tenth. "Well that's strange, the power readings are stable, no Belgium this time around."

"How is that possible?" said the fifth. "Is my TARDIS still here?"

"Yep, its out of phase like last time but you didn't pass through to it, like last time" said the tenth. "And the time differential caused by me has... changed your appearance somewhat."

The fifth doctor took out a small mirror and had a look at his face, which was aged over 20 years. He removed his hat but immediately put it back on when he noticed the bald spot near the back.

"So where are we?" the fifth asked.

"No idea, the TARDIS can't seem to get a lock on our location" said the tenth. "There's only one way to find out though". He went down to the TARDIS doors, grabbed his trenchcoat, donned it and then opened the TARDIS doors. The fifth doctor followed him outside. The TARDIS was parked between two large, half cylindrical shaped tents. In fact, the two time lords found themselves in the middle of a tent city.

"Possibly some kind of refugee camp" said the fifth. "Perhaps 3rd Dalek conflict? Or the Chozo wars?"

"Either time period we'd be able to identify from the TARDIS" said the tenth. "There's always the good old fashioned way". He walked out from between the tents onto a dirt road between several more tents. The Doctor could just spot the tops of several spaceships nearby and a few craft flew overhead, none of it familiar. A few structures were also being built in the distance.

"Defiantly not a refugee camp" said the fifth doctor as he noticed children playing and a few adults talking with one another. The conditions from the outside looked bad but the people didn't seem to mind, considering they all lived in tents. A vehicle rolled up that was strikingly familiar to the tenth doctor. Three people got out, dressed in nothing more than civilian clothes, they had armbands that bore the initials NCP, and they carried guns.

"Lets see some identification" the lead one said.

"Ah of course" said the tenth doctor as he reached into his coat pocket and removed his psychic paper. "I'm The Doctor and this... is... John Smith" he said pointing to the fifth doctor.

"Let me see that" said the leader as he snatched the paper away from The Doctor, unfortunately this broke the psychic connection and the illusion of a valid ID disappeared from the paper. "What the hell is this?" He said when he gave the paper back to The Doctor. "You two are coming with us for questioning."

They bound both doctor's hands and moved them to the back of the vehicle. The two doctors were forced to take a seat and ride with these unusual soldiers to their base.

"So much for 'the older the wiser'" the fifth grunted.

**

* * *

**

September 28, 2555

**location: Battlestar _Pegasus_**

With the sudden arrival of Colonel Sheppard and his team from their universe, Commander Adama halted the_ Pegasus'_ return trip until they could get a hold of the situation. Lee and Fred were meting with Sheppard and McKay in the commander's quarters while Ronon and Teyla guarded the jumper.

"So we went through the gate in our jumper and it..." Sheppard said, forgetting all the technobabble.

"The wormhole transported us to a Stargate in this universe" McKay finished for him.

"A Stargate?" Fred asked.

"I'm sure I explained the concept the last time I was here" said McKay.

"Please, doctor, indulge us" said Lee.

"Well in our universe, Stargates are ring shaped devices positioned on other planets. You can dial to another gate on another planet from one and the superconducting material that the gates are made up of can..."

"what Rodney is trying to tell you is that using the Stargates we can go to any planet with an joining gate, instantaneously" Sheppard finished.

"So one of these 'Stargates' was on Caprica?" Lee asked.

"Apparently" said McKay.

"Do you know why this Stargate would send you here?" Fred asked.

"There have been several incidents when the gate sent people to parallel universes, like for instance..."

"Rodney!" Sheppard hissed.

"We'll need to contact the Admiral before we do anything else" said Lee. "He'll have final decision on whether we can take you back to Caprica. In the mean time I can arrange quarters."

"That'll be fine for myself and Rodney, but I think Ronon and Teyla would prefer to stay on the jumper" said Sheppard.

"Have it your way" said Lee as the Lieutenant Colonel and McKay showed themselves out.

Lee turned to face Fred who was still clad in his MJOLNIR armor. The Spartan made the rookie Commander a bit nervous. During the battle of The Order homeworld, Lee had continued to be striped of his flight status and was assigned to _Pegasus_ damage control. He hadn't seen action in a viper since _Pegasus_ showed up. After the deaths of Commander Fisk at the hands of the black market and Commander Gardner during a Cylon ambush, Lee was given command of the mighty Battlestar by his father, Admiral Adama. Lee wasn't initially trusting of the UNSC, but after going to Earth himself and witnessing them in combat, he was starting to open up to them. They further gained his confidence after they began refitting _Pegasus_ with more advanced systems, but the refit was halted when the president and the Admiral decided to employ Admiral Cain's original strategy for fighting the Cylons, guerrilla war. It was hoped that the Cylons would be too busy licking their wounds to try and track down UNSC space. _Pegasus_ had been successful in the past month and just recently participated in the rescue mission for the Caprica resistance, with the assistance of the Spartans.

"What do you think, sir?" Fred asked.

"I think this is only getting started" said Lee. "From what you told me, the only time you meet people from parallel universes is when something big is going down. Or maybe they are just a bit lost."

"I don't think so" said Fred. "I can feel it."

--

Sheppard and McKay returned to the hangar bay and Sheppard signaled the all-clear to Teyla to open the jumper hatch. Sheppard and McKay went inside and Ronon closed the hatch behind them.

"What has the _Pegasus_ Commander decided?" Teyla asked.

"He has to contact his superiors first" said Sheppard.

"So there's a chance they could try and take the jumper?" McKay asked.

"With all the tech in here, who wouldn't?" Sheppard replied.

"Why didn't they just do it the last time?" Ronon asked.

"Well we had a common enemy, not to mention the _Daedalus_ on our side" said Sheppard.

"Then maybe we should consider trading some of our technology in exchange for their help" Teyla suggested.

"Or a look at their jump drive" said McKay.

"Rodney, why is that important?" Sheppard asked in an annoyed tone.

McKay retrieved his tablet PC, accessed a file from the directory and showed it to Sheppard. It had a complicated schematic and some writing in ancient.

"I found this in the Atlantis database" McKay said with a hit of excitement on his face. "It was an experimental propulsion system called 'wormhole drive'. And if I'm right, it could possibly provide instantaneous travel across vast distances. I've been trying to build a prototype and since the colonials use their folding space jump drives, the principal is basically the same. If I can get a look at their drive, I may be able to work out some of the kinks in my prototype."

"Rodney, remember the last time you tried to make an ancient failure work?" Sheppard asked.

"Well that was completely different" said McKay.

"Like ¾ difference" Sheppard said.

"Ha, ha" McKay replied.

"We'll sleep on it" said Sheppard as he went to the cockpit and shut the hatch behind him. Ronon, Teyla and McKay began bickering on who would get the seats in the back of the jumper while Sheppard simply propped his feet up on the seat behind the pilot's.

--

In another part of the Battlestar, one of the bunk rooms had been set up exclusively for the Spartans, directly across from an armory. Tom and Lucy were in one of the bunks, they had only removed their helmets before Tom swept Lucy up and into the bunk, then drew the curtains. They had spent the last few minutes kissing and now Tom was trying to work his armor off.

"Come on" Lucy said. "I thought we wouldn't do this while on a mission."

"But we're not on a mission" said Tom.

"But what if someone sees?" Lucy said with a smirk on her face.

"There's no one here" said Tom as he leaned in and kissed her again. But both of them were distracted when they herd a thud from inside the room. Lucy had been giggling over the past few minutes, so they both assumed they had been herd by someone else in the room. Tom opened the curtains so that both of their heads were visible. They saw Kelly sitting up against the bunk on the opposite side of the room, without her helmet and a long look on her face. She had never been the same since the Master Chief's death. Linda and the el-tee had told them stories of how the two of them were practically inseparable when they were younger. Since the funeral, she had become increasingly more isolated from everyone else. Fred and Linda dismissed it as stress caused by lack of combat over the past two months. Kelly lifted her head up in their direction.

"You're not going to tell anyone, right?" Tom asked.

"I didn't the first time" said Kelly, "what makes you think I'd start now?"

"Thanks" said Lucy as she drew the curtains. Kelly leaned her head back against the wall, thinking mostly about the Master Chief. John had his fair amount of luck, but it didn't do him any good this time. The door to the room opened and Fred stepped in, he walked over to Kelly and knelt next to her.

"Are we going back to Caprica?" She asked.

"It'll have to be up to the Admiral if we can take the ship back" said Fred. "Personally, I'd like to help Sheppard out."

"I just want to pop a few more of those Cylons" said Kelly.

"How are you doing?" Fred asked.

"Fine, sir" said Kelly.

"You're not fine" said Fred. "You're on the edge, putting yourself in danger on purpose, like that stunt you pulled, having Tom and Lucy help you flank a superior enemy force."

"If I recall, we beat that _force_ because of flanking them" said Kelly.

"Kelly, you're on edge, you're trying to keep something bottled up inside and its causing you to lash out."

"There's nothing wrong with me" Kelly said. "I'm perfectly capable of performing my duty". It took everything she had to try and keep a straight face, Fred had guessed the truth about her.

"Just get some rest" said Fred.

"I'm afraid there won't be much of that" said Lee as he strolled into the room. "We just got a slipspace data burst from the Galactica, we have a mission."

--

Fred called together Blue team in the pilot's briefing room where Commander Adama was going to give them the briefing. Tom and Lucy came in last, two minutes apart per Kelly's instructions, so they wouldn't be caught. The only Spartans missing from the team were Ash, Olivia and Mark whom ONI sent on yet another classified mission. Commander Adama entered the room with Captain Thrace and Major Shaw. The colonial officers took the seats on the front row while the Spartans stood off to one side.

"Galactica recently went on a mission to rescue a Raptor crew that went missing on a scientific survey Lee started, "when they arrived, they were attacked by these". On the screens behind him, several wedge shaped fighters appeared, along with schematics and alternate views. "They're mark I Cylon raiders."

"the ones from your first war with the Cylons?" Fred asked.

"Yes" Lee continued. "Our Cylon prisoner gave us information that these Cylons are part of some rogue group that went missing while trying to protect their first hybrid, which was an experiment that served as a prelude to the creation of human form. They haven't been seen or herd from for forty years."

"And this Cylon prisoner just happened to know that for a fact, this hybrid as your people?" Linda asked.

"Forty years ago, my father was on a mission to destroy this hybrid, he crashed inside the facility and made it out just as the Cylons escaped with it said Lee. He saw some horrible things that the Cylons did to captured human prisoners. He said its imperative that we rescue the civilians and destroy the hybrid's ship."

"Our main problem is going to be able to get in there and get out, undetected" said Shaw.

"So does that mean you want us on the mission, Major?" Fred asked.

Shaw let out a cute smile, "only if you feel like fracking up some toasters."

"We're in" said Fred. "And I think I can get us a way in, undetected."

--

Fred walked up to the green hatch and banged twice on it. It lowered and Fred was met by Ronon's gun which he lowered after Sheppard said it was ok.

"We need your help" Fred said to him.

**

* * *

**

September 29, 2555

**location: Battlestar _Pegasus_**

"Mr Hoshi, take the FTL drive off line and move us off" Lee ordered as he felt another thud from the ship's main batteries, firing off a salvo burst to obliterate a wave of Cylon raiders.

"We're still not picking them up on DRADIS" said Hoshi.

"Relax, Lieutenant" said Lee. "If we can't see them then its a good bet the Cylons can't."

--

In the cloaked puddle jumper, Colonel Sheppard and his team sat in the cockpit while the strike team under Major Shaw sat in the rear. The Major rose from her seat and walked to the cockpit with Kelly in tow, uncomfortable with just sitting around. She remembered the last time she was aboard a jumper, during the retreat from The Order homeworld, how she managed to take on a Cylon baseship. She ended up getting a headache a day later that had been attributed to the mental strain of flying the jumper. Just being in the craft gave her head a slight throb.

"How are we sure that they're still alive?" Ronon asked.

Sheppard brought up the HUD, much to the surprise of Major Shaw, and scanned the interior of the Cylon ship. Pegasus had done a good job of knocking out it's FTL drive. The HUD pulsed two green dots in the interior of the Cylon ship.

"There were four people in that Raptor" said Shaw.

"Lets just get those two out before the Cylons decide to do something about them" said Kelly.

The jumper slid in through one of the hangar bays and set down toward the back. Still cloaked, Sheppard lowered the ramp and Tom and Lucy went ahead to secure the entrance to the corridor. Sheppard placed Teyla, Linda, Tom and Lucy on guard duty, and Shaw led the rest of the group through the corridors. Sheppard was monitoring the two survivors on the lifesigns detector and led them to the hatch. Rodney ran a bypass on the door lock, saving them the option of trying to force the door and risk setting of an alarm. Fred entered first and swept the room, M7 in hand. Once clear, Sheppard and Ronon freed the two civilians and they proceeded back the way they came. But Kelly's motion tracker pulsed several red contacts. From around the corner came this silver plated robot, a Mk I Cylon centurion.

"Take cover!" Fred barked as he opened fire with his M7, the rounds pinging off the Cylon's armor. The centurion drew a sub machine gun and started firing, but didn't hit anyone as Ronon fired his weapon at the centurion's head. This unfortunately set off the general alarm and soon the rescue team was pinned down in a corridor, protecting from flanking sides.

"Thrace, the nuke!" Shaw commanded.

From her pack, Starbuck removed the half-sphere HAVOK tactical nuke, supplied to them by the UNSC to replenish the nearly depleted nuclear stockpile of the two battlestars. The casing had been grazed by a bullet and Fred and McKay were working on restoring the remote trigger. Kelly had just taken out another centurion when this voice sounded in her ears.

"_All this has happened before, and all of it will happen again."_

this voice distracted Kelly long enough for a centurion to step into the corridor, gun raised and pointed at her. But instead of firing, it said: Stop! In a synthesized, robotic voice. Everyone's heads turned in the centurion's direction.

"You will be allowed to leave, peacefully. So long as those two come with us". The centurion pointed to Major Shaw and Kelly.

"Absolutely not" said Fred.

"If you don't then this section will be decompressed" the centurion replied. "Those two will not be harmed."

"El-tee, just agree to it" said Kelly.

"No, we can fight our way past them" Fred retorted.

"Lieutenant, we're going with her on this" said Shaw. "Two people are worth the risk if we can get the rest of the team, and more importantly those we came here to get, out. Captain, the nuke."

Thrace handed the HAVOK to Kelly and then helped the civilians up. They were escorted along with the rest of Blue team, and Sheppard's team to the hangar bay while Kelly and Major Shaw were taken to a medium sized room where holographic codes ran along the walls. In the center of the room was an elderly man, half submerged in a tank of a strange white liquid. He was muttering something when they entered.

"The collection of beings will return to the place once burned, and the reclaimer will depart to finish his final task. In the midsts of the ensuing confusion, she will find him, and the subordinate will become a leader. When the great tear has been sealed, the leader will find himself home, but not the home he knows. They will meet the lost children of the reclaimer, and another lost child shall join their quest for an end to all that has happened before. The man of another Earth will realize his half self, and shall join in the quest to end the cycle and the search for those who are lost. The lost city will play a part in the final conflict with the knights of the great alliance. And to save existence, a battle must be waged at the place where ideas spring forth, one will die, and new life shall be formed."

"are you... a... god?" Shaw asked.

"What is a god, what defines a being of incredible power? Is a god one who has the power and does not interfere? Or is it one who rules in fear? You seek forgiveness, Kendra Shaw."

"I do" Shaw replied.

"Forgiveness for what?" Kelly asked.

"I did something... while Cain was in command" Shaw admitted.

"You also have a regret, Kelly-087" said the hybrid. "You blame yourself for something you should have done, something you should have said."

"Enough!" Kelly barked. She affixed the HAVOK to the side of the hybrid's tank and inserted the arming card. The LEDs pulsed green and the remote trigger, now repaired, linked to Kelly's HUD. "Major, let's get out of here."

Shaw turned to leave and swept the corridor, but just as Kelly turned to leave the hybrid's arm reached out and grabbed her armored one.

"The one you care about... he is not dead" the hybrid muttered.

Kelly shook free of the hybrid's grasp and backed out of the room. Shaw had finished checking the nearby corridor and Kelly took the lead back to the hangar bay, they didn't encounter a single centurion. And according to Kelly's HUD, the nuke wasn't being tampered with. The pair returned to the hangar bay and were led by a NAV marker to the jumper. They proceeded up the invisible ramp and into the jumper where Teyla and Linda were tending to the civilians. Kelly and Shaw entered the cockpit just as Sheppard lifted off and out of the hangar bay. _Pegasus_ could be scene in the distance, the number of Cylon raiders had diminished as the surviving fighters regrouped and scrambled into air defense positions around the hybrid's ship. Once clear, Kelly sent the signal through the jumper's subspace radio. The jumper was rattled around by the shockwave but the inertia dampers handled most of the rough stuff.

"What happened?" Fred asked.

"The hybrid" Shaw muttered. "The centurions took us to see the hybrid."

"What did it say to you?" McKay asked.

"Nothing" Kelly replied. "It was incoherent."

**

* * *

**

September 30, 2555

**location: Beta Indi system, New Caprica- Battlestar _Pegasus _**

_Pegasus_ approached a gas giant which was the fifth planet of this system. In a orbit between some of the planet's rings sat a blue green moon. This world had been scouted by the UNSC after the Covenant war as one of several potential colony sites, but was instead given to the colonials as a new homeworld, named New Caprica. In orbit of the planet was a small convoy of ships, those that were incapable of a planetary landing, the only thing is a fixed orbit was the _cloud 9_ passenger liner that was being converted into an orbital spaceport, part of president Roslin's plan to bring back the colonial economy, because they were dependent on the UNSC for just about everything. Also in orbit was the Spartan's def facto HQ, the UNSC _Ark Angel,_the ship was flanked by the frigates _Midway_ and _Cyprus._ Also traveling with them was a repair and refit station that currently held the Battlestar _Galactica,_ she was being refitted with newer titanium-A armor and archer missile pods in addition to upgrades to her point defense and main KEW batteries. Pegasus settled into an orbit at the lead of the remaining civilian ships, and launched the puddle jumper that held Commander Adama, Blue team, Kara Thrace and Colonel Sheppard's team. They were heading for the capital, and only city on the surface. It was little more than a tent city at this point, but a lot of prefab structures had been erected and foundations for more permanent ones were being constructed. The jumper set down on one of the landing pads of a military base on the outskirts of town where several ships from the fleet were parked, including_ colonial one._ The real facility existed underground where a bunker had been constructed with multiple sub levels, at the request of Admiral Adama. It currently housed the colonial government and the unofficial Earth embassy. Sheppard's team had to be relieved of their weapons before being showed to the elevator and sent down to sub level three, the president's office. The Spartans, in dress uniforms went in first and saluted, seated in the president's office was Captain Miranda Keyes, Admiral Adama and of course, president Roslin.

"Lieutenant, Captain" Roslin said. "Good job on the rescue."

"Thank you ma'am" said Fred.

"We received your first message" said Adama. "And unfortunately we can't spare _Pegasus_ to take you back to Caprica to find this supposed Stargate."

"And why is that?" Ronon said as he muscled his way to the front.

"Because its a decision for the new administration, one he's already said no to" said Roslin.

"The election?" Lee asked.

"He won" said Adama. "The absentee ballots from _Pegasus_ didn't make a difference."

"So I take it you've elected a new president?" Sheppard asked.

"Oh yes, Colonel" said another man who walked into the room, he wore a suit band had jet back hair.

"Saxon Hollow" he said as he extended his hand to Sheppard, "president-elect of the twelve colonies."

"Pleasure" Sheppard muttered without returning the handshake.

"I understand that you must be upset that we cannot facilitate your return to Caprica, but I cannot risk our only operational Battlestar on what might be a one way trip."

"Which is why I'm taking you instead, Colonel" said Keyes. "You can fly your ship to my cruiser, we're departing in three hours for Caprica."

"I appreciate it, Captain" said Sheppard, with a glare in the president-elect's direction. Sheppard and his team were escorted topside with the UNSC personnel. Once on the surface, Keyes led the Spartans away from the jumper.

"We have another situation" she said, "follow me."

Keyes led the Spartans across the base to the detention center that just went up, severals cells were still under construction. Keyes led the group over to the ones near the back, where two strangely dressed men sat.

"Doctor?!" Kelly said in surprise.

The tenth doctor stood up from the bench he was sitting on, "its nice to see a familiar face" he said. "How about getting me and my friend out of here?"


	6. Chapter 6: house guests

**Disclaimer: I don't own Halo or any other videogame or TV show in this fic**

**chapter 6: house guests**

**October 1, 2555**

**location: UNSC Ark Angel en route to Caprica**

Fred traversed the corridors of the cruiser to one of the cargo decks where a very important item was being stored. Fred nodded to the guards as he entered the cargo bay, in the middle of the room was the doctor's TARDIS. Fred never got a chance to get a look at the doctor's spaceship and had a hard time believing Donna Noble's description of it in their last encounter. Fred noticed the door was slightly ajar and curiosity getting the better of him, he pushed it open the rest of the way. An initial shock and awe, followed by a quick double check of the TARDIS's outer size made his jaw almost drop. The interior was roughly spherical, and had what looked like coral structures growing odd angled columns, it made the TARDIS look more alien than even some Covenant ships. Standing at the center console was The Doctor and his equally odd dressed friend who The Doctor only identified as John Smith. Absent though was Donna Noble.

"Its alright" The Doctor said when he noticed Fred in the doorway, "you can come inside".

Fred stepped up the ramp, surprisingly it was able to support his MJOLNIR armor. He walked up to The Doctor has he hunched over a monitor on the central console, it had a green glass shaft running down the middle.

"That's it" said John Smith as he pointed at the screen. "It looks like your TARDIS is drawing power from my TARDIS."

"That explains how we're still running in a parallel universe" said The Doctor.

"_His_ TARDIS?" Fred asked.

"Sorry" said The Doctor. "John Smith has his own TARDIS, and accidentally merged it with mine while flying it. And I have commented about his flying many times but he doesn't seem to listen."

John Smith shot a glare in the doctor's direction before returning to scrutinizing the screen.

"Just how big is this thing on the inside?" Fred asked.

"oh... big enough" The Doctor replied. "How are all those other guests you have?"

"Colonel Sheppard's team?" Said Fred. "They're a bit paranoid, probably because they're cut off and don't trust some people on this ship. Who wouldn't? ONI has operatives everywhere and I'm sure they'd love to get their hands on Sheppard's puddle jumper. Don't worry, Captain Keyes has guaranteed your protection so long as you're aboard, and I'll assign one of my team to guard the TARDIS."

"Oh, that won't be necessary. Those doors have kept out Genghis Kahn's Army, they can handle your ONI" said The Doctor.

"If you need something, ask the guards outside the door" said Fred as he left the TARDIS, making sure to shut the door behind him. Fred left the cargo bay and walked through the halls of the cruiser heading for the Spartan armory when he herd his name called. Turing around, he saw Major Shaw standing behind him.

"Major, I wasn't aware you were with us" Fred said.

"The Admiral thought you could use a military liaison since you might face the Cylons again" Shaw replied. "So I was picked by the Admiral."

"It'll be good to have your input, ma'am" Fred said.

"Kendra" said Shaw. "You don't have to call me ma'am, I understand you just do it as a sign of respect even though we're from a different military. Its ok to call me by my first name."

"ok... Kendra" Fred said, getting a weird feeling down his spine by doing so.

"Now then" said Kendra as she walked forward and looped her arm around Fred's armored one, "where can two people go to get a drink on this ship?"

--

In the Spartan armory, the rest of Blue team sat with Colonel Sheppard as they poured over an interesting video clip that Tom had dug up from the _Ark Angel's_ archives. It was a SPI armor helmet cam recording from Ash's helmet during the ONI mission to the Forerunner ruins, where they discovered The Order's plans. Tom found the description of a Stargate by doctor McKay strikingly familiar so after a foray into the ship's archives he brought the clip to Sheppard. After reviewing it once, Sheppard called up doctor McKay who was now scrutinizing the image.

"Yeah, that's a gate alright" McKay said. "But there's something different about it."

"The chevrons, Rodney!" Sheppard pointed out.

The Spartans leaned in closer to get a better look, along the ring were six triangular shaped crystal lights, glowing an eerie purple. Engraved in what looked like a stone track on the ring were several different symbols which McKay wasn't able to identify.

"The gate's usually have local star constellations engraved on them" McKay explained. "But something about these gates are different aside from their chevrons."

"They kinda look like milky way models" Sheppard said. "Maybe those Forerunners developed the tech themselves, Beckett proved that the Ancients and Forerunners were the same race."

"But their tech is different" Linda said. "There's no evidence that proves they developed similar technologies. The odds of them designing identical pieces of technology are astronomical."

"Suppose you're right there" McKay muttered.

"Maybe we can find some evidence" said Tom as he went over to a terminal and activated it. The ship's artificial intelligence, Falkland, appeared in his usual avatar of a bald eagle. He ruffled his feathers before looking up at Tom.

"Spartan-B292, what can I help you with today?" He asked.

"Falkland, I need the Forerunner records Olivia downloaded 3 months ago, and any colonial historical records involving a great stone ring" Tom asked.

Doctor McKay came over to the terminal and transferred the Forerunner files to his tablet PC, then began scrutinizing them.

"I'm going to have to get a dell from the jumper" McKay said. "This encryption scheme is complex."

"But you can break it?" Tom asked. "ONI hasn't had any luck cracking it."

"Not a problem" McKay said quickly as he hurried out of the room, still working on his tablet. Tom turned his attention to the colonial records, part of the deal of this alliance was a cultural exchange so the _Ark Angel_ had a copy of the history of the twelve colonies on board. Lucy came over and joined Tom at the station. She smiled a bit.

"You were always the smart one" she said to him. "Adam and Min always thought so."

Tom chuckled a bit, "I always thought you were the smart one, you were always so clever during training."

Lucy leaned on Tom's arm, "Tom, do you ever wonder what we'd do when this is all over?"

"Huh?"

"All this fighting, I mean the Cylons can't be a threat forever" said Lucy. "The rebels have been loosing support, soon there's not going to be a need for Spartans."

"Maybe" Tom muttered. "But I'll have you, what more could I want to do with my life?"

Neither of them caring that they were in plain view of the others in the room, Lucy leaned her head on Tom's shoulder. She sat up when the computer had finished Falkland's search and the results were displayed on the screen. The text identified the ring object as a supposed religious artifact left by their gods during the exodus of the thirteen tribes. Tom accessed a picture of the artifact and sure enough it was a Stargate. The same model they saw on Ash's log.

"Hey, guys" Tom called out, drawing Sheppard and Linda over to them. Kelly had disappeared.

"According to this, the gate here is over 4000 years old" said Lucy.

"And I think I know why" said doctor McKay has he reentered the armory, with a gray dell laptop in hand. The Spartans and Sheppard gathered around McKay as he set the laptop down on the table.

"Rodney, what do you have?" Sheppard asked.

"I was able to decipher the encryption rather quickly' McKay explained. "This particular file had a rather low key encryption than some of the other files so I was able to write a bypass..."

"Rodney!"

"Ok, ok, I managed to find records of a Forerunner scout vessel that discovered a crashed ship on a moon, it was defiantly Ancient, and it was full of Stargates."

"How did an Ancient ship full of strange Stargates end up in a parallel universe?" Sheppard asked.

"You got me" said McKay. "Also, the facility that The Order was using to abduct people from parallel universe was a research facility studying the gates.

"So the question still is, how did an ancient ship get to this universe?" Sheppard said.

"How about how you got here in the first place" said Tom. "Let alone how to get back."

"I've been thinking about that" said McKay as he turned around in his chair to face them. "We're going to have to find the DHD and determine if its been configured in any way. We should also probably look for anything hooked up to the gate that effects an parallel universe dial."

"Rodney, how did we dial to it in the first place?" Said Sheppard. "The address we dialed from Atlantis was defiantly to a Pegasus gate."

"Did anyone see where Kelly went?" Linda asked. "Let alone what happened to Fred?"

"Let the be if they want" said Sheppard. "We've got a big day ahead of us."

--

Kelly had enough of all this strange Stargate stuff and decided to get some rest. The Spartans had each been assigned their own separate cabin on the same deck as their armory, so she didn't have far to walk. Kelly entered her room and began removing her MJOLNIR armor, the whole process taking about forty minutes. She immediately collapsed on the bed after removing the last plate and matte layer. She tried to find a comfortable spot on the bed, but it wasn't the bed that was contributing to her insomnia as much as it was the hybrid's words to her.

"John is dead" she told herself. "That thing was just trying to mess with your head, it was just guessing how you felt."

**

* * *

**

January 18, 2261

**location: Epsilon Eridani system, Epsilon III- USS _Gettysburg_**

It had been three days since the _Gettysburg_'s arrival in what the crew had nicknamed 'the Babylon universe'. All of the crew had subsequently been revived from stasis and the ship was slowly returning to normal, except for the whole being cut of from their home universe thing. In one of the guest quarters, Samus was going over the diagnostics of her varia suit, using one of the Starfleet tricorders that Commander Collins had loaned her. Also in her cabin were boxes of equipment and other effects she had been able to salvage from her gunship. She had also donated the ship to be scrapped for raw materials by the Gettysburg's crew, considering it was nothing more than a useless hulk of bulkheads and fried electronics. There was an audible chime throughout the room and it took Samus a minute to realize it was the doorbell. She crossed the room and opened the door to find the Master Chief standing there, clad in a Starfleet uniform.

"Master Chief, I wasn't expecting you. Nor did I know you _were _a member of the crew."

"I'm not" John replied. "This is a disguise."

"Sneaky" Samus smirked. "So do you need a parter in crime or something?"

"I thought you'd want to get off the ship for a while, see the station?"

"Babylon 5? Samus asked, she had seen the station through her window and the thought of checking it out did intrigue her. "Are you sure that Cheney guy is willing to let me roam off the ship?"

"I already asked the Captain" said John. "So?"

"I guess" said Samus.

"Here" said John as he handed her a uniform that was tucked underneath his arm. "Put it on."

--

A few minutes later, the Chief and Samus were in the transporter room, Samus and the Chief dressed in matching uniforms, each bearing a Starfleet Master Chief's insignia on their tunics.

"Remind me why we're in these uniforms?"

"Captain's orders" said John. "And we can be tracked by the _Gettysburg_ through the communicators."

"Excuse me, ma'am" said an Ensign who came up and planted a hypo on her neck.

"Its a sub dermal transmitter, just in case out communicators are taken' John explained.

Is there something you're not telling me about this station?" Samus asked.

"Well the Captain was warned about crime rates on the station" John explained. "He said anyone who wanted to visit the station should be warned to keep on the look out, who knows who'd want to jump us for our advanced tech."

"Point taken" Samus replied.

"Standby for transport" said the technician.

Samus became ridged, this being her first transporter experience that she was actually conscious for. The swirling blue columns of light surrounded her body and she watched as the transporter room fade away and was replaced by a sea of blue fuzzy light. This eventually resolved into a corridor of a unknown design. The light disappeared and Samus could feel her body again. John was right next to her and noticed her become disoriented, and managed to catch her before she fell. She looked up at John as he held her close, and her face turned a shade of red. The Chief let her go and they proceeded down the corridor and into a main room. Samus could see that this room in fact was curved and followed the symmetry of the station, so she assumed this room was along the outer hull. This area was lined with shops and various alien species Samus hadn't seen before. They set about exploring the shops, not knowing they were being watched by Cortana and Commander Baker. Those two had also come to visit the station and while browsing in the Zocalo, Cortana spotted John with Samus. She and Baker were watching the two of them from a concealed position in one of the side passages.

"What is he doing with her?" Cortana said.

"He's probably being a good host" Baker said. "Stop overreacting."

"Maybe he is looking for someone else" Cortana muttered.

"Why are you jumping to the worst case?" Baker asked.

"He hasn't been the same, ever since An'Lok captured him, ever since he made John..."

"Hey" Baker said as she put a hand on her shoulder. "You shouldn't think about stuff like that. He was brainwashed into doing those things."

"I think its changed him" Cortana whispered. "Say, what's with the crowd?"

Various alien species began converging in the Zocalo,drawing the attention of John and Samus. John saw Minbari ambassador Delenn enter the room so he decided to ask her what was going on. But before he got the chance his communicator chirped.

"_Anderson to Master Chief"_

"go ahead, Captain."

"_We've got an unidentified ship approaching the station and from what Commander Ivanova just told me, its using Babylon 5's access codes to initiate docking procedures. B5 is going on full security alert and I'm recalling all away parties from the station. Prepare for transport."_

"Negative, Captain. Something is happening down here" John replied. "Take everyone else but my party."

"_Very well, Chief" _Anderson replied. "_If things get hot on B5 then I'm going to have to take the Gettysburg out of range."_

John turned his attention to Delenn who noticed his presence.

"You are the Master Chief?" She asked. "The security officer Captain Anderson spoke of."

"I am" John replied.

"Delenn needs your protection" said her companion, a male Minbari.

"Lennier, I do not require..." Delenn started before she was cut off by the Drazi ambassador standing on the catwalk above the Zocalo.

"Everyone listen, listen to us! There's something that you don't know and we must tell you the truth he bellowed. Because the Minbari don't tell you the whole truth. Delenn and others are conspiring against all of your lives by organizing an attack against the home world of the shadows."

John and Samus moved closer to Delenn to protect her in case the mob turned violent.

"The shadows have withdrawn for now, there have been no new attacks. We believe we can find a peaceful solution. If there is another pointless attack against Za'ha'dum they will destroy us all!"

"They will come anyway!" Delenn finally barked.

"You don't know that!" The Drazi ambassador spat back.

"It has been a thousand years since the last shadow war, if we do nothing to provoke them it may be another thousand years before they move again" said the other alien ambassador. "We cannot allow the fleet to leave for Za'ha'dum."

"That fleet is our only chance" Delenn pleaded.

"Don't listen to her, she must be silenced."

The crowd took this as an invitation to attack her, and one eager Drazi moved toward her, stopped by a blow to the chest by John that caused the alien to double over. Samus handled the crowd from behind while Lennier handled the left and right.

"You are acting out of fear!" Delenn yelled.

"And you're acting out of grief and loss the other ambassador said. "Sheridan has died then why not the rest of us. You cannot attack Za'ha'dum, no one has ever succeeded. Ships go there and never return. Lives are wasted. Sheridan died trying to attack Za'ha'dum, no one who goes there comes back alive."

John watched as Delenn looked up in shock, along with everyone else. John and Samus looked up to see a man walk across the catwalk toward the ambassadors, he wore a B5 uniform similar to Ivanova's, though his was tattered and riped on the sleeves. The ambassadors seemed surprised to his presence.

"C-captain... we're sorry... we thought you were dead" said the Drazi ambassador.

It suddenly all made sense to John, this man was Captain Sheridan, the man who died trying to attack Za'ha'dum!

"I was" Sheridan started, "I'm better now. The ambassador is correct, I went to Za'ha'dum, I've seen the face of the enemy and they're not gods and they're not indestructible. I've fought them and I've killed many of them... and I've survived. There is a way out of this, to stop this insanity once and for all. Now Delenn's fleet is a start, now we have to build on it. Together we shall form the largest fleet in history, not just for a battle but to change the shape of the galaxy. Not just for ourselves but for our children, and our children's children."

John saw Delenn slip away.

"Tell your governments that the only man to survive Za'ha'dum sends this message: we can end this! Not just for now, not just for the next thousand years, but forever! I stand before you as proof that it can be done. We can fight and we can win, but only if we do it together. Can I count on you?"

The crowd began to cheer in support of Sheridan.

"Can I count on you, will you stand together?" He bellowed and the whole crowd erupted in cheers for Sheridan.

John watched as Delenn emerged on the catwalk and embraced Sheridan.

"So the two of them are involved, huh?" Samus commented. "They make a cute couple."

John looked over at Samus as she had a small smile on her face for the happy reunion.

**

* * *

**

October 2, 2555

**location: the twelve colonies system, Caprica- UNSC Ark Angel**

"Falkland, any sign of detection?" Captain Keyes asked from her command chair.

"Negative, ma'am" the AI replied. "Out polar orbit appears to be obscuring any Cylon DRADIS. We shouldn't be detected.

"Doctor, are you sure you can extract our people undetected?" Keyes asked the tenth as he stood on the bridge, the fifth staying in the TARDIS. Their plan was to have Colonel Sheppard and Blue Team find the Stargate, secure it and protect doctor McKay as he attempted to discover what went wrong with the gate, and whether or not they could return.

"Ma'am, I'm detecting a fluctuation in the planet's ionosphere, near the pole" said Falkland.

"Its possibly a cause of all the radiation in the atmosphere" Keyes said. "I've never seen a planet this contaminated."

"Captain, I'm sure this isn't..."

The AI was cut short as the cruiser was rocked by multiple missile impacts.

"Five Cylon baseships just appeared out of nowhere, Captain!" The NAV officer replied.

"Weapons, return fire!" Keyes barked.

"Its no good, Captain" the weapons officer replied.

"Shields are down to sixty-three percent, the magnetic field of the poles is interfering with the emitters. I cannot guarantee I can keep shield integrity stable for much longer."

Keyes weighed her options, but knew she couldn't rule out the only logical course of action if Blue Team managed to succeed, but that opened up another opportunity for survival.

--

In the puddle jumper, Sheppard intercepted communication from the _Ark Angel_ and had Fred come up to the cockpit. The HUD activated and a readout of the polar region appeared.

"Cylons, what the hell!" McKay said as he double checked to see if the sensors were working properly.

"How could this happened?" Teyla said.

"They would have had to know where the _Ark Angel_ was going to be" said Fred. "With the ship that low in the pole it would have scrambled the Cylon DRADIS."

"Hang on, she's climbing" said McKay as they watched the blip that represented the _Ark Angel_ climb out of the polar region, then disappear off the screen.

"What happened!? Was she destroyed?" Fred said.

"There's a residual background radiation consistent with a slipspace jump" McKay said as he studied the readings.

"John, there!" Said Teyla as she spotted the building that housed the Stargate. Fred hit the magnification on his visor and caught sight of the ring shaped device.

"Doctor, I don't see this DHD thing you said is supposed to be right next to it" Fred said.

Suddenly, the jumper was shook as rounds began impacting the hull, while the Ancient craft was still under cloak. Sheppard deactivated the cloak and banked left.

"Rodney, dial Atlantis! Sheppard said as he brought the jumper back around.

'Sheppard, we don't even know if..." McKay protested.

"Those machines saw through our cloak, we can't land to see if the gate is usable!" Sheppard said.

McKay reluctantly agreed and Fred watched as he hit seven symbols on the center panel, then hit the large one at the bottom of the panel.

"What's going on?" Kelly asked as she wandered into the cockpit in time to see the chevrons on the gate light up, followed by a whoosh of energy that resolved into what appeared to be water suspended in the center of the gate.

"Sorry, but it looks like you're coming home with us for a while" said Sheppard. "Rodney, your GDO."

McKay removed a small device from his vest pocket and typed in a numerical sequence. Kelly herd the drive pods retract into the jumper, followed by it making contact with the event horizon. It happened in a flash, the puddle seemed to penetrate a jumper and Kelly saw it happen due to the delayed reaction, often called Spartan Time. The puddle touched and enveloped her and Kelly found herself on a roller coaster ride through some kind of green energy tunnel that wound through the stars. There was another flash and he felt her body again. She was still in the jumper but the scenery had changed outside. Out of the windscreen she could see a staircase that had odd writings on it, this led up to a balcony of some sort dominated by a large, stained glass window.

"Raise the shield!" Sheppard barked into the radio. The gate shield went up around the event horizon of the Atlantis Stargate, and blocked the pursuing raiders and centurions that tried to pass through. Then the wormhole shut down. The jumper began to rise up into the overhead jumper bay.

"Welcome to Atlantis" Sheppard said to the Spartans.

**

* * *

**

October 3, 2555

**location: Beta Indi system, New Caprica- president's office**

"Mr president, we have a situation" said new appointed Chief of staff, Felix Gaeta said as he strolled into the president's office, closing the door behind him.

"Felix, what can I help you with?" Said newly sworn-in, president Hollow.

"Sir, you know about the slipspace data burst transmitter the UNSC installed?" Felix asked.

"Yes, remarkable piece of equipment" said Hollow.

'Mr president, I've found evidence that someone sent a message directed in the area of Caprica, containing the energy signature of the UNSC Ark Angel."

He handed the president a file folder of his evidence as he stood up in surprise.

"This is everything you have?" He asked.

"Yes, sir, I didn't know who to trust with this" said Gaeta.

"You did the right thing, son" said Hollow as he sat back down and pulled a mask over his face.

"Sir, what is that?" Gaeta asked.

The president said something that was muffled by the mask.

"What?" Gaeta said.

The president pulled it away from his mouth for a moment and said "its a gas mask", before putting it back on.

"Why do you need a gas mask, sir?" Gaeta asked.

The president said another muffled word before pulling it away and saying "because of the gas". Then he put it back on.

"What gas?" Gaeta asked.

Hollow said something that sounded an awful lot like "this gas". Suddenly, the halon fire suppressant activated and the room flooded with deadly halo fire suppressant. Gaeta collapsed to the floor, holding his throat as he slowly convulsed, then died. Hollow removed his mask and began tapping his middle and index finger on the table, in a four tone beat.

**message from the general: **ha ha, poor Gaeta, but peg-leg deserved it!


	7. Chapter 7: the pegasus project

**Disclaimer: I don't own Halo or any other videogame or TV show mentioned in this fic**

**Chapter 7: the Pegasus project**

**August 5, 2008**

**location: Pegasus galaxy, M5S-117, Atlantis base**

Fred stood in the Atlantis conference room with Linda and Kelly as they awaited Colonel Sheppard's return. The perfectly circular room made Fred feel like he was in a prison cell rather than a conference room. A plasma screen stood on a rolling rack behind the large, wooden conference table that had been set up in the room. Tom and Lucy were sent under Fred's orders to the room the Atlantis leader had arranged for Blue Team, someone Fred had yet to meet. The five doors that separated the room from the rest of Stargate operations opened and three people stepped inside, Fred caught a glimpse of the four guards stationed outside and another look at the control room that the Spartans had been led away from after being taken from the jumper bay, surrendering their weapons and escorted here. Two of the people who entered were Colonel Sheppard and doctor McKay, but the third wore a different uniform, was balding and had a pair of glasses on his strikingly familiar face. None of the Spartans spoke up as he stood at the end of the table.

"I'm Richard Woolsey, Commander of the Atlantis expedition. Which one of you is Lieutenant Frederick?"

"I am, sir" Fred said as he stepped forward and saluted.

"You can have a seat" Woolsey said as he Sheppard and McKay sat down.

"Sir, these chairs cannot support the weight of our armor" Fred said.

"Very well then" Woolsey said as he opened the file folder containing Colonel Sheppard's report. "Let me first stress that we are sympathetic to your situation and we will do everything possible to send you home, but first we need to find out how you came to be here in the first place."

"Why don't you just activate your Stargate to the one on Caprica and send us back?" Linda asked.

"I've suspended gate travel until we can determine what exactly caused out Stargate to jump to a parallel universe. If this is a sign of some kind of problem with the gate, there's a good chance that this could lead to a more serious situation. I can't risk using the Stargate for the safety of everyone on the base."

"So for the time being you're just going to have to stick around" said Sheppard.

"I'll have Colonel Sheppard escort you to your quarters" said Woolsey as he stood up and exited the conference room. Fred, Kelly and Linda stepped out of the circular room and into Stargate operations. From the balcony, Fred could see the Atlantis Stargate and its different design, it was more reminiscent of something digital with its star constellation symbols and blue chevrons. Behind it was a beautiful stained glass window that mirrored the one at the top of the stairs. Fred was also able to get an unobstructed view of the Atlantis control room, there were five main consoles in the room, situated in front of a display screen that was suspended in the middle of the room. Also present was technology that was consistent of 21st century Earth, computer server towers and plasma screen displays. Linda was also admiring the design.

"Its something else" Sheppard said as he joined them.

"How old is this place?" Linda asked.

"Well from what Rodney tells me, pretty damn old. We should probably get going" said Sheppard.

"Where's Kelly?" Linda said when she noticed she had slipped away. Sheppard pointed toward the main window, standing on the outside gallery was Kelly as she looked over the side. Sheppard led Fred and Linda over to the door and they joined Kelly on the gallery where they got a breathtaking view of part of the city. There were buildings of alien architecture surrounding the main tower, the city itself was roughly shaped like a snowflake with five piers extending outward from the main tower. The ocean stretched on for as far as the eye could see. Sheppard eventually led them back inside and they watched ad Dr McKay left Stargate operations, mumbling on about how he had to help someone, another guest, with their database research. Sheppard took them through the hall until they arrived at what appeared to be a closet when the door opened, but a recessed panel activated and a map of the city appeared.

"Its a transporter" Sheppard explained. "We can get across the city faster."

Because of the transporter's small size, Sheppard had to shuttle the Spartans in their MJOLNIR armor, one at a time. Once everyone was across the city, Sheppard escorted them through a large hall and up a staircase, then across an upper level. As they walked down the hall, Kelly stopped when her eye caught sight of a peculiar room. It was roughly circular, had a display on one wall and a control panel on the opposite side. Dominating the center of the room however was a chair of ancient design.

"Colonel, what's this?" She asked when Sheppard and the others turned back to see why she had stopped.

"That the control chair" Sheppard explained. "It allows us to control the city's weapons systems and stardrive."

"Stardrive? You mean it can fly?" Fred asked.

"Well, yeah" Sheppard said as they moved on. "The city is designed to fly, its got this shield that can keep the atmosphere in, inertia dampners, sublight and hyperspace engines."

"So why don't you just fly it to Earth, why keep it in another galaxy?" Linda asked.

"Power. Its designed to run on three of these things we call ZPMs, and we only have one running the city. Plus we can't exactly leave with the wraith roaming the galaxy."

"The what?" Kelly asked.

"Never mind" Sheppard said as they reached the room the Spartans were assigned. Sheppard waved his hand over the three crystal, control panel mounted next to the door and it slid open. Inside were several pieces of furniture arranged in a large sitting room with access to a deck overlooking part of the pier. Sitting in front of their weapons was Tom and Lucy who stood at attention when Fred entered the room.

"Sir, the Atlantis Marines returned our weapons, we're just inspecting them" Tom said.

Fred nodded and Kelly and Linda proceeded inside, but Sheppard held Fred back.

"Look, Woolsey is leaving on the _Daedalus_ for a meeting with one of our allies in a few hours, so that means I'm in charge."

"But I'm guessing you're not going to lift the ban on using the Stargate?" Fred asked.

Sheppard made a long face and said "no, Woolsey's right, we gotta figure out why the Stargate is dialing to parallel universes before we risk using it again."

Fred nodded in agreement and Sheppard left the room, the door shutting behind him.

--

The sun of M5S-117 had set and its two visible moons shown bright in the night sky. Kelly leaned up against one of the railings on their deck, letting the sea breeze blow across her exposed head, her helmet sat next to her on the floor. Kelly looked out across the city as it glowed like some of the metropolises of the former outer colonies. Kelly herd the glass door behind her open as Fred stepped out onto the balcony.

"Its so peaceful here" Kelly whispered.

"I know, this city is amazing" Fred replied. "Its a shame Dr. Halsey isn't here to see it."

"She'd be lording over that McKay guy for hours" Kelly commented. "Sir, do you think we're going to be able to go home?"

"This city is supposed to be full of scientists who know about this Stargate, plus that McKay guy seems to be the expert around here."

"Don't let him hear that" Kelly said.

"You're doing better" Fred said.

"I'm what?"

"You're not acting strangely, not since we arrived" Fred explained. "Do you want to tell me what was bothering you before?"

Kelly took a deep breath and prepared to meet Fred's gaze when a strange sound drew her and Fred's attention. A shimmering energy field suddenly appeared around the city's perimeter and extended to cover Atlantis like a dome.

"What's going on?" Kelly said.

"I think this is the Atlantis shield" Fred said. "But why are they raising it?"

"Out there" Kelly said as her enhanced vision caught sight of a small ship as it approached the city, and passed through the shield, taking up position over the adjacent pier. Fred activated his visor's magnifications and saw the front of the ship's belly open up.

"What is it?" Kelly said, "another ship the Atlantis expedition has?"

Fred saw three figures drop from the belly of the ship and impact the tower, punching clean through. Whoever they were, they weren't invited, it explained why Atlantis would activate its defensive shield.

"Let's go, the city is being invaded" Fred said as he wrenched the door open, Kelly hot on his tail. They acquired their MA5Bs and were out of the room before they had a chance to alert Linda, Tom and Lucy. They found a transporter and Fred hit the part of the city that this ship was hovering over. When they emerged they herd gunfire from down the hall, so they broke out at an near sprint. When they arrived at the source they were just in time to see a blue blur punch through the floor, Colonel Sheppard, Teyla and a team of Marines stood with G36 assault rifles over the hole.

"What's at the bottom of this tower?" Sheppard asked Teyla.

Teyla looked over at him in dread and said "Rodney."

"what's going on, who were those guys?" Kelly asked.

"No time, we have to move" Sheppard said as he led the Marines along with Fred and Kelly down several flights of stairs to the lower part of the pier. The hallways were coated with sea salt which indicated that this room was at one time partially flooded. As they ran through the halls, Sheppard explained what was down there.

"Rodney and another scientist from Earth, Dr Jackson discovered a hidden lab that belonged to an ancient."

"Jackson, I remember him" Fred said. "He was with SG-1 when they helped us take down ONI."

"So this lab is what the aliens are after?" Kelly asked.

"That's a good bet" Sheppard said as they rounded the corner to find an armored person standing in the middle of the hall. The armor was reminiscent of MJOLNIR, but in no way looked identical. The alien raised his left forearm and activated something on it, he held it out to the side and a gold energy barrier that reminded the Spartans of a jackal's energy shield appeared and he used it to block the incoming weapons fire. As they continued firing, two aliens seemed to emerge from the wall at the end of the corridor holding a piece of technology, and the unconscious Doctors Jackson and McKay. They carried them onto a circular platform that was positioned below the hole in the ceiling. A blue energy field sprang up around the two aliens and Jackson and McKay, then the whole thing shot up through the hole all the way to it's ship. The other alien's shield failed and their combined firepower penetrated its armor, killing it. Sheppard, Teyla, Fred and Kelly cautiously approached the fallen alien.

"Control room, what's the status of that ship?" Sheppard asked over the radio.

"_I'm sorry, Colonel. They're gone."_

--

An hour later, Fred and Kelly were still guarding the dead alien, now with the additional help of Linda, Tom and Lucy. A team of scientists arrived, led by a middle aged man with brown thinning hair and glasses.

"Is it alive?" He asked in a Slavic accent.

"You tell me" Sheppard replied. "This is Doctor Zelenka by the way" he said to Fred.

"Uh, yes... its a pleasure" he said rather quickly, having just realized the armored Spartan's presence. He took out a handled Ancient scanner and scanned the alien. "No. I'm not getting any coherent readings. Perhaps we should put it under a medical scanner."

"Ok, do it" Sheppard said.

"Go get a gurney" Zelenka said to one of the other scientists. As the scientist heads off, Zelenka looked up at the hole in the ceiling. "Ooh! So is it true they took Rodney and Doctor Jackson?"

"Yeah" Sheppard replied.

The other scientist returned with a gurney and Fred and Kelly helped load the heavy alien onto it, then escorted it to a lab where one of the Ancient medical scanners had been delivered. The Spartans stood guard for several minutes, Kelly walked over to the alien and found a weapon still attached to it's holster. She removed the weapon and inspected it, it was roughly shaped like the old stun-guns that were sometimes used on the Spartans during their training.

"Do you think these are those Wraith that Sheppard was talking about?" Kelly asked.

"Could be" Fred said. "But if their ships can easily penetrate the city's shields the it would have made sense to just wipe it out a long time ago. What do you have there?"

"Dunno, probably its weapon" Kelly said as she gripped it as if she was going to use it, and accidentally triggered it. The gun fired a yellow energy pulse that hit the wall and dispersed.

"Let's not try that again" she said as she set the weapon down on the table. Colonel Sheppard, Doctor Zelenka and Teyla arrived shortly there after, and after the first unsuccessful attempt to scan it, Sheppard ordered it be cut open. Zelenka tried the chest plate with a power saw, unsuccessfully, and after Sheppard suggested trying the neck, Zelenka was starting to make some progress, until Kelly noticed something on the chest plate.

"Stop!" she called out, and gave them enough time to hear the whine emitting from the armor that slowly grew faster.

"Get out! Everyone, get out!" Sheppard cried.

The Spartans and Atlantis personnel bolted for the door, Kelly grabbing the alien's gun as they ran out of the lab, down a short hall and ducked behind a corner as fire and debris raced after them.

"Everyone ok?" Sheppard asked.

"Yes" Teyla replied after making sure everyone got out ok.

"Somebody really wants to keep secret whatever's inside that suit" Sheppard said.

"Could you use this to figure out who?" Kelly asked as she handed the alien gun over to Sheppard.

"Radek?" Shepard asked Zelenka.

"Well if I could gain access to the power source then I could run a tr..."

Kelly cut him off as she retook the gun from Sheppard, grabbed hold of the grip and tore the gun open, handing the small yellow power cell to Zelenka.

"Yes, yes, this will take a few hours though" Zelenka said.

"Put someone else on it" said Sheppard.

--

The Spartans returned to their quarters at the request of Colonel Sheppard, Fred had volunteered Blue Team for security work on the base which Sheppard had to turn down, citing the Spartans weren't familiar with the city's layout. Eventually, Sheppard returned towards the evening, suited up for a mission.

"We've got a location of where the aliens took Rodney and Doctor Jackson, still feel like volunteering?"

"Where do you need us?" Fred asked, Kelly, Linda, Tom and Lucy also jumped into action. Passing out their remaining weapons and ammunition, which was still a considerable amount. Once ready, Sheppard brought them to the armory and issued them USAF weapons, just in case their assault rifles ran out. After stocking up and waiting for Teyla and the Marines to arrive, Sheppard led the group to the jumper bay, along the way he explained the plan.

"The planet Rodney and Daniel are being held has no Stargate, so we're going to gate as close to the _Daedalus_ as we can, have them pick us up and take us the rest of the way."

"Aren't you taking a risk by using the Stargate?" Fred asked. "McKay didn't say anything about finding out the problem before he was kidnapped, did he?"

Sheppard didn't say anything else as they entered the jumper bay, and walked over to the closest jumper. Doctor Zelenka was standing inside the aft compartment, closing up several crystal trays in the ceiling.

"Ok, all set. So I'll have Chuck dial M5R-179 and you should be able to contact the Daedalus via sub-space once you get there" Zelenka said as he left.

Sheppard, Teyla, Fred and Kelly went to the front of the jumper while everyone else settled in the rear. They waited a minute before Sheppard began to power up the puddle jumper, but suddenly Zelenka's voice broke in on the radio.

"_Colonel, do not lower the Jumper into the Gateroom."_

"Why not?"

"_Well, for some reason there is an unprecedented power build-up within the Gate."  
_  
"Power build-up from where?"

"_It's coming from within the event horizon. Oh, no. This is very, very bad for us."_

"Just shut it down. It's probably a faulty Gate at the other end."

"_I'm-I'm-I'm trying! It won't let me!"_

After several seconds of silence Sheppard said: "All right, I'm coming down."

Kelly began to feel concerned that the Atlantis expeditions about there being something wrong with the gate were being realized. She and the others quickly hurried to the control room where Colonel Sheppard immediately assumed control of the situation.

"What do we do? Wait thirty-eight minutes and ride the puddle out?"

"I wish. If the power continues to build like this, the Gate will reach critical overload and most certainly explode" said Zelenka.

"Explode?! How the hell can it explode" Fred asked?

"I _told_ you it was very, very bad for us" Zelenka said quickly.

"How did something like this happen? How _can_ it happen?" Kelly asked.

"I don't know. It's never happened before" said Zelenka.

"How long do we have?" Sheppard asked.

"Not very long at all. About ninety seconds" Zelenka said.

"Ninety seconds?!" Teyla hissed.

"I would say closer to sixty" said a female technician.

"We've gotta evacuate everyone in the tower" said Fred. "Get them to a safe distance?"

"The Gate exploding is the equivalent of a dozen nuclear explosions. There's nowhere we could evacuate quickly enough to a safe distance" said Zelenka.

"And you people actually use this technology safely?!" Tom said.

"The-the-the shield" Sheppard said as he snapped his fingers together frantically. "Collapse the city's shield around the Gate; we can contain the explosion."

"Yes, yes. That might just work" Zelenka said as she scooted his chair over to another station and began typing frantically. Kelly turned to looked down at the Atlantis Stargate and herd the familiar noise of the Atlantis shield as it slowly formed a bubble around the active Stargate. Another technician began counting down the seconds they had left till it explodes.

"The Gate'll reach a critical limit in five, four, three, two". The shield reached the top of the gate just as he said: "...one."

A brilliant yellow light fills the room and everyone cowered as the gate explodes, thankfully contained inside the shield. The Spartan's visors automatically tinted so they were able to witness the swirling patters inside the protective bubble. Kelly's heart jumped when her radiation meter began flickering wildly.

"Don't look at the blast!" Zelenka cried.

"Could've mentioned that before!" Sheppard said.

"I'll see if I can divert more power to the shield, see if we can block more of the radiation."

He typed and the shield whined as it strengthened around the destroyed Gate. Sheppard lowered his hand and walked closer to the balcony, looking down at the yellow ball of energy inside the field. Kelly's radiation meter flickered and slowly dropped to safe levels.

"Ok, now what?" Fred asked.

"Well, the shield continues to diffuse the energy of the blast" Zelenka explained. "Every second that it is contained within the shield, the explosion gets weaker."

"How long does it take?" Sheppard asked.

An alarm beeped and Zelenka's eyes widened.

"Oh no. The shield needs at least another minute to contain the full brunt of the blast, but we're frying out the emitters. I don't know how much longer I can hold this."

"Shut down the city. Transfer all the power" Sheppard said.

"Yes, I'm trying."

"Everyone who doesn't need to be here, get to the edge of the city. Move! Everybody!" Sheppard called out to the others in the Control Room.

He spoke briefly with Teyla before she joined the exodus from the tower. Kelly was the last one out, but had a change of heart before she was even halfway down the stairs and raced back into the control room.

"Tell me what you need to do with the controls" she said. "Then you two get out of here."

"What?!" Said Sheppard. "Are you nuts."

"If the shield fails then I stand the best chance of surviving a blast, Spartans are built a lot tougher."

"Its not a matter of strength" said Zelenka. "I cannot possibly tell you how to regulate shield power in time."

"Look, there a transporter over in that hall" Sheppard said as he pointed to the exit on the other side of the gate room. "Go, now, that's an order!"

Kelly knew she couldn't win so she took off down the main staircase, heading for the exit before it was too late. She looked back on where the Stargate was, the yellow glow began to fluctuate and fill with orange speckling, the explosion was becoming weaker. Kelly was about to round the corner, and her armor's audible alarm was the last thing she herd.

--

Several levels down, Teyla, Fred and Linda were exiting a transporter.

"Move quickly!" Teyla said to the people in the hall. "We have to get everyone to the lower levels of the tower to make sure that everyone will be ..."

She stops as an explosion goes off several levels above. People scream and duck as the tower shakes and the lights go out. At the top of the tower, the windows of the control room blow out.

"Colonel Sheppard, are you all right?" She asked over the radio. "John!?"

The head duty nurse ran towards the group.

"Teyla, how many were up there?" She asked.

"I'll go get my people" she replied as she hurried off to assemble a medical team. Tom and Lucy approached Fred and Linda, having come from a different transporter.

"Is Kelly with you?" Tom asked.

"We thought she was with you" Linda replied.

Fred looked at Linda for a moment before turning to Teyla.

"Better make that... three."

--

A few minutes later, the rescue team arrived in what was left of the gate room, a large crater stood as testament to where the Stargate once resided. The window behind it was gone as was practically every other window in the tower, including the one at the top of the stairs. Fred tried to get a lock on Kelly's IFF, with no luck. The rescue team entered the control room which was a mess of overturn consoles, large chunks of debris and broke glass.

"They were right here when I left them" said Teyla.

"If the explosion was hot enough, there might not be anything left for us to find" said the nurse.

"Over here" said Tom as he leaned through the broken window frame and saw Colonel Sheppard lying protectively over Doctor Zelenka. Tom bounded through the frame and slowly helped Sheppard up.

"We didn't take cover" he groaned.

"Are you ok, Colonel?" Tom asked.

"Huh?"

"Are you ok?" Tom repeated.

"Oh, my ears. I think I got some glass in my back."

"Take him" Tom said to a pair of medics who assisted Sheppard to the infirmary. Tom then focused on helping Doctor Zelenka back up, who was putting his glasses that were miraculously unbroken, back on.

"We lost the Stargate. We lost the control room in the blast" he mumbled.

"Be grateful you're still here" Tom said as he also passed Zelenka off to medics, and climbed back inside the debris strewn room to search for Kelly, which didn't take long.

"Lieutenant!" Lucy screamed from over near the briefing room. The Spartans reached there first and found Kelly lying face down on the far side of the balcony. Fred looked up and found an impression in the ceiling, Kelly was most likely propelled upward by the blast, hit that spot and landed here. Fred and Linda helped Kelly up and brought her down the stairs, heading for the transporter. As they passed the crater where the Stargate once was, Fred realized with the gate gone they were going to be here for a while.


	8. A message from the author

Ok folks, sorry to disappoint, but I'm afraid this might be the end for the _Universes Collide_ series, at least for right now.

I've looked back on what has been written for the current installment and I'm starting to become disappointed on how this is turning out. It seems I can't captivate my readers with a good storyline as your reviews and hits have become sparse over the past few weeks.

I am also myself going through some tough personal turmoil and haven't found it in my heart to write for the last week or two on any of my stories.

So here's what I have planned for right now, _Universes Collide 3: Shadow Conflicts_ is going to be suspended pending a possible total re-write of the _Universes Collide_ series. I have no intention of deleting these stories and I will leave _Universes Collide 3_ the way it is right now.

My other fics won't be affected so they will continue normally.

I feel like I've failed you in some respects as this story doesn't seem to be popular enough to warrant attention. I would greatly appreciate your input as readers on what the fate of this story should be so feel free to leave a review or even drop me a PM

thanks, General MB


End file.
